@article{zhang_zentella_burkey_liao_tisdale_2024, title={Long-term tropospheric ozone pollution disrupts plant-microbe-soil interactions in the agroecosystem}, volume={30}, ISSN={["1365-2486"]}, DOI={10.1111/gcb.17215}, abstractNote={Abstract}, number={3}, journal={GLOBAL CHANGE BIOLOGY}, author={Zhang, Kaile and Zentella, Rodolfo and Burkey, Kent O. and Liao, Hui-Ling and Tisdale, Ripley H.}, year={2024}, month={Mar} }
 @article{zentella_burkey_tisdale_2023, title={Impact of tropospheric ozone on root proteomes of two soybean genotypes with contrasting sensitivity to ozone}, volume={208}, ISSN={["1873-7307"]}, DOI={10.1016/j.envexpbot.2023.105269}, abstractNote={Tropospheric ozone (O3), a critically harmful greenhouse gas, has steadily increased over the last several decades, leading to significant soybean (Glycine max) yield loses worldwide. However, substantial efforts have focused on the effect of elevated O3 concentration (eOZ) on shoots rather than the roots that support plant fitness and directly interact with soil ecosystems. To better assess the impact of eOZ on roots, this study investigated morphological and proteomic profiles of two soybean genotypes from the same genetic background, but with contrasting O3 resilience, Fiskeby III (O3-tolerant) and Fiskeby 840–7–3 (O3-sensitive). Plants were treated either with sub-ambient O3 or eOZ in a field-based air exclusion system (AES) and harvested at flowering and pod-filling stages. Our results established that the effect of eOZ on decreasing root biomass initiated at the flowering stage, while above-ground biomass was not altered. However, O3-caused biomass reduction was observed in both, roots and shoots, at the pod-filling stage. Season-long eOZ ultimately caused a 29 % seed yield reduction in Fiskeby III, and 50 % in Fiskeby 840–7–3. Root proteome analysis showed that the effect of O3 in roots is complex, and distinct between flowering and pod-filling stages. Changes in the abundance of proteins correspond to glycolysis, TCA cycle, nitrogen metabolism, secondary metabolites, antioxidant, and stress response pathway, and differed between genotypes. Some of these changes may be in response to eOZ as an attempt to mitigate the effects of a challenging environment, and others are likely due to genetic differences that confer an adaptative advantage to the O3 resilient genotype. These findings provide further knowledge of proteins and pathways that may confer O3-tolerance, which can be applied to develop O3-resistant, high-yielding soybean.}, journal={ENVIRONMENTAL AND EXPERIMENTAL BOTANY}, author={Zentella, Rodolfo and Burkey, Kent O. and Tisdale, Ripley H.}, year={2023}, month={Apr} }
 @article{zhang_zentella_burkey_liao_tisdale_2023, title={Microbial community dynamics responding to nutrient allocation associated with soybean cultivar ?Jake? ozone adaptation}, volume={864}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2022.161008}, abstractNote={Tropospheric ozone (O3), a major air pollutant, leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. Soybean cultivar ‘Jake’ shows O3 resilient traits in above-ground organs, but the root system remains sensitive to elevated O3 (eO3). Changing carbon (C) and nitrogen (N) resource composition during eO3 stress suggests that eO3 presumably alters belowground soil microbial communities and their driven nutrient transformation. Yet, the responses of belowground microbes to eO3 and their feedback on nutrient cycling in ‘Jake’ are unknown. In this study, we holistically investigated soil microbial communities associated with C and N dynamics and bacterial-fungal inter-kingdom networks in the rhizosphere and bulk soil at different developmental stages of ‘Jake’ grown under sub-ambient O3 [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or eO3 (12 h mean: 87 ppb). The results demonstrated eO3 significantly decreased fungal diversity and complexity of microbial networks at different ‘Jake’ developmental stages, whereas bacterial diversity was more tolerant to eO3 in both bulk soil and rhizosphere. In the bulk soil, no O3-responsive microbial biomarkers were found to be associated with C and N content, implying eO3 may stimulate niche-based processes during ‘Jake’ growth. In contrast, this study identified O3-responsive microbial biomarkers that may contribute to the N acquisition (Chloroflexales) and C dynamics (Caldilineales, Thermomicrobiales, and Hypocreales) in the rhizosphere, which may support the O3 resilience of the ‘Jake’ cultivar. However, further investigation is required to confirm their specific contributions by determining changes in microbial gene expression. Overall, these findings conduce to an expanding knowledge base that O3 induces temporal and spatial changes in the effects of microbial and nutrient networks in the O3-tolerant agriculture ecosystems.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Zhang, Kaile and Zentella, Rodolfo and Burkey, Kent O. and Liao, Hui-Ling and Tisdale, Ripley H.}, year={2023}, month={Mar} }
 @article{livingston_tuong_tisdale_zobel_2022, title={Visualising the effect of freezing on the vascular system of wheat in three dimensions by in-block imaging of dye-infiltrated plants}, ISSN={["1365-2818"]}, DOI={10.1111/jmi.13101}, abstractNote={Abstract}, journal={JOURNAL OF MICROSCOPY}, author={Livingston, David and Tuong, Tan and Tisdale, Ripley and Zobel, Rich}, year={2022}, month={Apr} }
 @article{tisdale_zentella_burkey_2021, title={Impact of elevated ozone on yield and carbon-nitrogen content in soybean cultivar 'Jake'}, volume={306}, ISSN={["1873-2259"]}, DOI={10.1016/j.plantsci.2021.110855}, abstractNote={Tropospheric ozone (O3) is a pollutant that leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. To ensure soybean productivity in areas of rising O3, it is important to identify tolerant genotypes. This work describes the response of the high-yielding soybean cultivar ‘Jake’ to elevated O3 concentrations. ‘Jake’ was treated with either low O3 [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or with O3-enriched air (12 h mean: 87 ppb) over the course of the entire growing season. In contrast to the absence of O3-induced leaf injury under low O3, elevated O3 caused severe leaf injury and decreased stomatal conductance and photosynthesis. Although elevated O3 reduced total leaf area, leaf number, and plant height at different developmental stages, above-ground and root biomass remained unchanged. Analyzing carbon and nitrogen content, we found that elevated O3 altered allocation of both elements, which ultimately led to a 15 % yield loss by decreasing seed size but not seed number. We concluded that cultivar ‘Jake’ possesses developmental strength to tolerate chronic O3 conditions, attributes that make it suitable breeding material for the generation of new O3 tolerant lines.}, journal={PLANT SCIENCE}, author={Tisdale, Ripley H. and Zentella, Rodolfo and Burkey, Kent O.}, year={2021}, month={May} }
 @article{tisdale_zobel_burkey_2021, title={Tropospheric ozone rapidly decreases root growth by altering carbon metabolism and detoxification capability in growing soybean roots}, volume={766}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2020.144292}, abstractNote={High tropospheric ozone (O3) concentrations lead to significant global soybean (Glycine max) yield reductions. Research concerning O3 impacts on soybean has focused on the contributions of above-ground tissues. In this study, Mandarin (Ottawa) (O3-sensitive) and Fiskeby III (O3-tolerant) soybean genotypes provide contrasting materials to investigate O3 effects on root growth. We compared root morphological and proteomic changes when 16-day-old plants were treated with charcoal-filtered (CF) air or elevated O3 (80 ppb O3 for 7 h/day) in continuously stirred-tank reactors (CSTR) for 7 days. Our results showed that in Mandarin (Ottawa), decreased expression of enzymes involved in the tricarboxylic acid (TCA) cycle contributes to reduction of root biomass and diameter under elevated O3. In contrast, O3 tolerance in Fiskeby III roots was associated with O3-dependent induction of enzymes involved in glycolysis and O3-independent expression of enzymes involved in the ascorbate-glutathione cycle. We conclude that a decreased abundance of key redox enzymes in roots due to limited carbon availability rapidly alters root growth under O3 stress. However, maintaining a high abundance of enzymes associated with redox status and detoxification capability contributes to overall O3 tolerance in roots.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Tisdale, Ripley H. and Zobel, Richard W. and Burkey, Kent O.}, year={2021}, month={Apr} }
 @article{burkey_tisdale_zobel_ray_pursley_2020, title={Interactive Effects of Elevated Ozone and Temperature on Growth and Yield of Soybean (Glycine max (L.) Merr.) under Field Conditions}, volume={10}, ISSN={["2073-4395"]}, DOI={10.3390/agronomy10111803}, abstractNote={Elevated ozone and rising temperature are both factors in climate change, but they are difficult to study in combination due to exposure system requirements. We developed and deployed an air exclusion exposure system to treat soybean (Glycine max (L.) Merr.) cultivar “Jake” with season-long combinations of sub-ambient ozone (18 ppb, 12 h mean), elevated ozone (66 ppb, 12 h mean), and elevated temperature (+3.5 °C daytime, +2.4 °C nighttime) in irrigated field plots. Warming caused a shift in biomass partitioning from reproductive tissues into stems and petioles at mid-season that resulted in a significant 25% reduction in final seed yield and a significant reduction in harvest index. The elevated ozone treatment delayed mid-season biomass production, and final seed yield was reduced by a non-significant 2%. However, there were significant underlying effects of elevated ozone on seed production. The non-significant impact of ozone on seed yield of cultivar “Jake” resulted from significant increases in pod number (+16%) and seed number (+18%) that were offset by a significant reduction in seed size (−16%). No evidence of significant warming–ozone interactions was found in biomass or seed yield responses. In general, significant impacts of the individual warming or ozone treatments were found to be additive.}, number={11}, journal={AGRONOMY-BASEL}, author={Burkey, Kent and Tisdale, Ripley and Zobel, Richard and Ray, Samuel and Pursley, Walter}, year={2020}, month={Nov} }
 @article{hsieh_chu_wolfinger_2007, title={Comparison of statistical performance of univariate and bivariate mixed models for Affymetrix (R) probe level data}, volume={77}, ISSN={["0094-9655"]}, DOI={10.1080/10629360600826398}, abstractNote={Half of the probes on Affymetrix® microarrays contain a single base mismatch (MM) of a known perfect match (PM) target sequence. While putatively designed to detect nonspecific binding, the MM data can also contain true signals and because of this, debates persist concerning how to best combine PM and MM data for statistical modeling purposes. Most current approaches involve either subtracting some function of MM from PM or ignoring MM altogether. Here, we describe a bivariate model that includes both PM and MM based on the mixed linear modelling framework. It directly models the correlation between PM and MM and thereby increases the power of significant gene detection. In this paper, we show that the bivariate mixed model offers moderate gains in power over a comparable univariate model that ignores the MM data. The gains are more prominent when the number of replicates and the array-to-array variability is small. We apply the models to a small experiment on yeast and use the data as a basis for a Monte Carlo simulation.}, number={3}, journal={JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION}, author={Hsieh, Wen-Ping and Chu, Tzu-Ming and Wolfinger, Russ}, year={2007}, pages={251–264} }
 @article{hsieh_passador-gurgel_stone_gibson_2007, title={Mixture modeling of transcript abundance classes in natural populations}, volume={8}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2007-8-6-r98}, abstractNote={Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes of abundance among individuals within populations.Expression profiling using cDNA microarrays was conducted in Drosophila melanogaster adult female heads for 58 nearly isogenic lines from a North Carolina population and 50 from a California population. Using a mixture modeling approach, transcripts were identified that exhibit more than one mode of transcript abundance across the samples. Power studies indicate that sample sizes of 50 individuals will generally be sufficient to detect divergent transcript abundance classes. The distribution of transcript abundance classes is skewed toward low frequency minor classes, which is reminiscent of the typical skew in genotype frequencies. Similar results are observed in reported data on gene expression in human lymphoblast cell lines, in which analysis of association with linked polymorphisms implies that cis-acting single nucleotide polymorphisms make only a modest contribution to bimodal distributions of transcript abundance.Population surveys of gene expression may complement genetical genomics as a general approach to quantifying sources of transcriptional variation. Differential expression of transcripts among individuals is due to a complex interplay of cis-acting and trans-acting factors.}, number={6}, journal={GENOME BIOLOGY}, author={Hsieh, Wen-Ping and Passador-Gurgel, Gisele and Stone, Eric A. and Gibson, Greg}, year={2007} }
 @article{hsieh_chu_wolfinger_gibson_2003, title={Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles}, volume={165}, number={2}, journal={Genetics}, author={Hsieh, W. P. and Chu, T. M. and Wolfinger, R. D. and Gibson, G.}, year={2003}, pages={747–757} }