@article{walsh_tollison_brochu_shaw_diveley_chou_law_kirk_gale_peng_2022, title={Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques}, volume={208}, ISSN={["1550-6606"]}, url={https://doi.org/10.4049/jimmunol.2100824}, DOI={10.4049/jimmunol.2100824}, abstractNote={Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.}, number={3}, journal={JOURNAL OF IMMUNOLOGY}, author={Walsh, Evan S. and Tollison, Tammy S. and Brochu, Hayden N. and Shaw, Brian I and Diveley, Kayleigh R. and Chou, Hsuan and Law, Lynn and Kirk, Allan D. and Gale, Michael, Jr. and Peng, Xinxia}, year={2022}, month={Feb}, pages={762–771} }
 @article{chou_jima_funk_jackson_sweeney_buchwalter_2020, title={Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-75064-y}, abstractNote={Abstract To better understand the effects of transient thermal stress in an aquatic insect, we first identified static temperatures associated with fitness deficits, and then reared larvae from egg hatch to adulthood under diurnally variable regimens including daily forays into deleterious temperatures. We sampled mature larvae at the coolest and warmest portions of their respective regimens for RNA-seq analysis. Few transcripts (28) were differentially expressed when larvae oscillated between favorable temperatures, while 614 transcripts were differentially expressed when experiencing daily transient thermal stress. Transcripts associated with N -glycan processing were downregulated while those associated with lipid catabolism and chitin turnover were significantly upregulated in heat stressed larvae. An across-regimen comparison of differentially expressed transcripts among organisms sampled at comparable temperatures demonstrated that the effects of daily thermal stress persisted even when larvae were sampled at a more optimal temperature (806 differentially expressed transcripts). The chronically stressed population had reduced expression of transcripts related to ATP synthesis, mitochondrial electron chain functions, gluconeogenesis and glycolytic processes while transcripts associated with cell adhesion, synaptic vesicle transport, regulation of membrane potential and lipid biosynthesis increased. Comparisons of constant vs. variable temperatures revealed that the negative consequences of time spent at stressful temperatures were not offset by more time spent at optimal temperatures.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Chou, Hsuan and Jima, Dereje D. and Funk, David H. and Jackson, John K. and Sweeney, Bernard W. and Buchwalter, David B.}, year={2020}, month={Nov} }
 @article{buchwalter_scheibener_chou_soucek_elphick_2019, title={Are sulfate effects in the mayfly Neocloeon triangulifer driven by the cost of ion regulation?}, volume={374}, ISSN={["1471-2970"]}, DOI={10.1098/rstb.2018.0013}, abstractNote={
            Elevated major ion concentrations in streams are commonly observed as a consequence of resource extraction, de-icing and other anthropogenic activities. Ecologists report biodiversity losses associated with increasing salinity, with mayflies typically being highly responsive to increases of different major ions. In this study, we evaluated the performance of the mayfly
            Neocloeon triangulifer
            reared for its entire larval phase in a gradient of sulfate concentrations. Two natural waters were amended with SO
            4
            as a blend of CaSO
            4
            and MgSO
            4
            and exposures ranged from 5 to 1500 mg l
            –1
            SO
            4.
            Survival (per cent successful emergence to the subimago stage) was significantly reduced at the highest SO
            4
            concentration in both waters, while development was significantly delayed at 667 mg l
            −1
            SO
            4
            . Final sub-adult body weights were consistent across treatments, except at the highest treatment concentration. Despite evidence for sulfate uptake rates increasing with exposure concentrations and not being saturated at even extremely high SO
            4
            concentrations, total body sulfur changed little in subimagos. Together, these results suggest that elevated SO
            4
            imposes an energetic demand associated with maintaining homeostasis that is manifested primarily as reduced growth rates and associated developmental delays. We identified two genes related to sulfate transport in
            N. triangulifer
            .
          }, number={1764}, journal={PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Buchwalter, David and Scheibener, Shane and Chou, Hsuan and Soucek, David and Elphick, James}, year={2019}, month={Jan} }
 @misc{rodriguez-celma_chou_kobayashi_long_balk_2019, title={Hemerythrin E3 Ubiquitin Ligases as Negative Regulators of Iron Homeostasis in Plants}, volume={10}, ISSN={["1664-462X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85062388289&partnerID=MN8TOARS}, DOI={10.3389/fpls.2019.00098}, abstractNote={Iron (Fe) is an essential nutrient for plants, but at the same time its redox properties can make it a dangerous toxin inside living cells. Homeostasis between uptake, use and storage of Fe must be maintained at all times. A small family of unique hemerythrin E3 ubiquitin ligases found in green algae and plants play an important role in avoiding toxic Fe overload, acting as negative regulators of Fe homeostasis. Protein interaction data showed that they target specific transcription factors for degradation by the 26S proteasome. It is thought that the activity of the E3 ubiquitin ligases is controlled by Fe binding to the N-terminal hemerythrin motifs. Here, we discuss what we have learned so far from studies on the HRZ (Hemerythrin RING Zinc finger) proteins in rice, the homologous BTS (BRUTUS) and root-specific BTSL (BRUTUS-LIKE) in Arabidopsis. A mechanistic model is proposed to help focus future research questions towards a full understanding of the regulatory role of these proteins in Fe homeostasis in plants.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Rodriguez-Celma, Jorge and Chou, Hsuan and Kobayashi, Takanori and Long, Terri A. and Balk, Janneke}, year={2019}, month={Feb} }
 @article{chou_pathmasiri_deese-spruill_sumner_jima_funk_jackson_sweeney_buchwalter_2018, title={The Good, the Bad, and the Lethal: Gene Expression and Metabolomics Reveal Physiological Mechanisms Underlying Chronic Thermal Effects in Mayfly Larvae (Neocloeon triangulifer)}, volume={6}, ISSN={["2296-701X"]}, DOI={10.3389/fevo.2018.00027}, abstractNote={Temperature dictates the performance of aquatic ectotherms. However, the physiological and biochemical processes that drive thermally-mediated life history patterns (and limits) remain poorly understood because they are rarely studied simultaneously. In our previous work, we have established life history outcomes (e.g. survivorship, development time, growth rates and fitness) in mayflies (Neocloeon triangulifer) reared at static temperatures ranging from 14°C - 30°C at 2°C intervals. In this study, we conducted biochemical measurements (RT-qPCR of select genes and targeted, quantitative metabolomic profiling) on N. triangulifer mature larvae reared at temperatures associated with excellent survival and fitness (22-24°C), compromised survival and fitness (28°C), and chronic lethality (30°C -larvae survived for a few weeks but failed to emerge to adulthood). Patterns of gene expression were similar to those observed in acute ramping experiments reported previously: larvae reared at 30°C resulted in significant upregulation in the thermally responsive gene HEAT SHOCK PROTEIN 90 (HSP90) but no significant changes in hypoxia responsive genes (EGG LAYING DEFECTIVE 9 (EGL-9) and LACTATE DEHYDROGENASE (LDH)). Additionally, primers for genes associated with energy: INSULIN RECEPTOR (IR), mechanistic TARGET OF RAPAMYCIN (mTOR) and TREHALOSE 6 PHOSPHATE SYNTHASE (T6PS) were developed for this study. IR and mTOR were significantly upregulated while T6PS showed trend of downregulation in larvae reared at 30°C. Metabolomic profiles revealed general depletion of lipids and acylcarnitines in larvae exposed to chronic thermal stress, suggesting that larvae were energetically challenged despite continuous access to food. For example, concentrations of lysoPhosphatidylcholine (lysoPC) a C20:3 decreased as fitness decreased with increasing temperature (2.3 fold and 2.4 fold at 28 and 30°C relative to controls). Tissue concentrations of the biogenic amine histamine increased 2.1 and 3.1 fold with increasing temperature, and were strongly and negatively correlated with performance. Thus, both histamine and lysoPC a C20:3 are potential biomarkers of thermal stress. Taken together, our results primarily associate energetic challenge with thermally mediated fitness reduction in N. triangulifer.}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, author={Chou, Hsuan and Pathmasiri, Wimal and Deese-spruill, Jocelin and Sumner, Susan J. and Jima, Dereje D. and Funk, David H. and Jackson, John K. and Sweeney, Bernard W. and Buchwalter, David B.}, year={2018}, month={Mar} }
 @article{chou_funk_buchwalter_2017, title={Keep breathing: Linking respiration to thermally regulated life history outcomes in the Mayfly Neocloeon triangulifer}, volume={57}, journal={Integrative and Comparative Biology}, author={Chou, H. and Funk, D. and Buchwalter, D.}, year={2017}, pages={E225–225} }
 @article{chou_pathmasiri_sumner_buchwalter_2017, title={Linking physiological mechanisms to thermally driven life history outcomes in the Mayfly Neocloeon triangulifer}, volume={57}, journal={Integrative and Comparative Biology}, author={Chou, H. and Pathmasiri, W. and Sumner, S. and Buchwalter, D.}, year={2017}, pages={E225–225} }
 @article{chou_pathmasiri_deese-spruill_sumner_buchwalter_2017, title={Metabolomics reveal physiological changes in mayfly larvae (Neocloeon triangulifer) at ecological upper thermal limits}, volume={101}, ISSN={["1879-1611"]}, DOI={10.1016/j.jinsphys.2017.07.008}, abstractNote={Aquatic insects play critical roles in freshwater ecosystems and temperature is a fundamental driver of species performance and distributions. However, the physiological mechanisms that determine the thermal performance of species remain unclear. Here we used a metabolomics approach to gain insights into physiological changes associated with a short-term, sublethal thermal challenge in the mayfly Neocloeon triangulifer (Ephemeroptera: Baetidae). Larvae were subjected to a thermal ramp (from 22 to 30 °C at a rate of 1 °C/h) and metabolomics analysis (both Nuclear Magnetic Resonance (NMR) Spectroscopy and Gas Chromatography coupled Time-of-Flight Mass Spectrometry (GC-TOF-MS)) indicated that processes related to energetics (sugar metabolism) and membrane stabilization primarily differentiated heat treated larvae from controls. Limited evidence of anaerobic metabolism was observed in the heat treated larvae at 30 °C, a temperature that is chronically lethal to larvae.}, journal={JOURNAL OF INSECT PHYSIOLOGY}, author={Chou, Hsuan and Pathmasiri, Wimal and Deese-Spruill, Jocelin and Sumner, Susan and Buchwalter, David B.}, year={2017}, pages={107–112} }
 @article{kim_chou_funk_jackson_sweeney_buchwalter_2017, title={Physiological responses to short-term thermal stress in mayfly (Neocloeon triangulifer) larvae in relation to upper thermal limits}, volume={220}, ISSN={["1477-9145"]}, DOI={10.1242/jeb.156919}, abstractNote={ABSTRACT}, number={14}, journal={JOURNAL OF EXPERIMENTAL BIOLOGY}, author={Kim, Kyoung Sun and Chou, Hsuan and Funk, David H. and Jackson, John K. and Sweeney, Bernard W. and Buchwalter, David B.}, year={2017}, month={Jul}, pages={2598–2605} }
 @article{chou_zhu_ma_berkowitz_2016, title={The CLAVATA signaling pathway mediating stem cell fate in shoot meristems requires Ca2+ as a secondary cytosolic messenger}, volume={85}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13123}, abstractNote={Summary}, number={4}, journal={PLANT JOURNAL}, author={Chou, Hsuan and Zhu, Yingfang and Ma, Yi and Berkowitz, Gerald A.}, year={2016}, month={Feb}, pages={494–506} }