Research Project: Soybean Seed Improvement Through Translational Genomics, Assessments of Elemental Carbon Metabolism, and Lipid Profiles

Location: Plant Genetics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism - (Peer Reviewed Journal)
Kambhampati, S., Hubbard, A.H., Koley, S., Gomez, J.D., Marsolais, F., Evans, B.S., Young, J.D., Allen, D.K. 2024. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Communications Biology. 7. Article 172. https://doi.org/10.1038/s42003-024-05844-z.

Program for integration and rapid analysis of mass isotopomer distributions (PIRAMID) - (Peer Reviewed Journal)
Gomez Castro, J.D., Wall, M.L., Rahim, M., Kambhampati, S., Evans, B.S., Allen, D.K., Antoniewicz, M.R., Young, J. 2023. Program for integration and rapid analysis of mass isotopomer distributions (PIRAMID). Bioinformatics. 39(11). Article btad661. https://doi.org/10.1093/bioinformatics/btad661.

Physcomitrium patens response to elevated CO2 is flexible and determined by an interaction between sugar and nitrogen availability - (Peer Reviewed Journal)
Mohanasundaram, B., Koley, S., Allen, D.K., Pandey, S. 2024. Physcomitrium patens response to elevated CO2 is flexible and determined by an interaction between sugar and nitrogen availability. New Phytologist. 241(3):1222-1235. https://doi.org/10.1111/nph.19348.

GmMFT: A potential step forward in soybean breeding for high oil and yield - (Other)
Mukherjee, T., Tully, T., Allen, D.K. 2023. GmMFT: A potential step forward in soybean breeding for high oil and yield. New Phytologist. 239(3):815-817. https://doi.org/10.1111/nph.18950.

Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans - (Peer Reviewed Journal)
Morley, S.A., Ma, F., Alazem, M., Frankfater, C., Yi, H., Burch-Smith, T., Clemente, T.E., Veena, V., Nguyen, H., Allen, D.K. 2023. Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans. New Phytologist. 239(5):1834-1851. https://doi.org/10.1111/nph.18835.

Depleting cationic lipids involved in antimicrobial resistance drives adaptive lipid remodeling in Enterococcus faecalis - (Peer Reviewed Journal)
Rashid, R., Nair, Z.J., Chia, D.M., Chong, K.K., Gassiot, A.C., Morley, S.A., Allen, D.K., Chen, S.L., Chng, S.S., Wenk, M.R., Kline, K.A. 2023. Depleting cationic lipids involved in antimicrobial resistance drives adaptive lipid remodeling in Enterococcus faecalis. mBio. 14(1). https://doi.org/10.1128/mbio.03073-22.

Metabolic synergy in Camelina reproductive tissues for seed development - (Peer Reviewed Journal)
Koley, S., Chu, K.L., Mukherjee, T., Morley, S.A., Klebanovych, A., Czymmek, K.J., Allen, D.K. 2022. Metabolic synergy in Camelina reproductive tissues for seed development. Science Advances. 8(43). Article eabo7683. https://doi.org/10.1126/sciadv.abo7683.

Comparative metabolic analysis reveals a metabolic switch in mature, hydrated, and germinated pollen in arabidopsis thaliana - (Peer Reviewed Journal)
Wang, J., Kambhampati, S., Allen, D.K., Chen, L. 2022. Comparative metabolic analysis reveals a metabolic switch in mature, hydrated, and germinated pollen in arabidopsis thaliana. Frontiers in Plant Science. 13. Article 836665. https://doi.org/10.3389/fpls.2022.836665.

Suppression of SDP1 improves soybean seed composition by increasing oil and reducing undigestible oligosaccharides - (Peer Reviewed Journal)
Aznar-Moreno, J.A., Mukherjee, T., Morley, S.A., Duressa, D., Kambhampati, S., Chu, K.L., Koley, S., Allen, D.K., Durrett, T.P. 2022. Suppression of SDP1 improves soybean seed composition by increasing oil and reducing undigestible oligosaccharides. Plant Biotechnology Journal. 13. Article 863254. https://doi.org/10.3389/fpls.2022.863254.

An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids - (Peer Reviewed Journal)
Koley, S., Chu, K.L., Gill, S.S., Allen, D.K. 2022. An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids. Journal of Experimental Botany. 73(9):2938–2952. https://doi.org/10.1093/jxb/erac062.

Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves - (Peer Reviewed Journal)
Chu, K.L., Koley, S., Jenkins, L.M., Bailey, S.R., Kambhampati, S., Foley, K., Arp, J.J., Morley, S.A., Czymmek, K., Bates, P.D., Allen, D.K. 2022. Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves. Metabolic Engineering. 69:231-248. https://doi.org/10.1016/j.ymben.2021.12.003.

Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves - (Peer Reviewed Journal)
Chu, K.L., Koley, S., Jenkins, L.M., Bailey, S.R., Kambhampati, S., Foley, K., Arp, J.J., Morley, S.A., Czymmek, K.J., Bates, P.D., Allen, D.K. 2021. Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves. Plant Physiology. 69:231-248. https://doi.org/10.1016/j.ymben.2021.12.003.

Sterile spikelets contribute to yield in sorghum and related grasses - (Peer Reviewed Journal)
Aubuchon-Elder, T., Coneva, V., Goad, D.M., Jenkins, L.M., Yu, Y., Allen, D.K., Kellogg, E.A. 2020. Sterile spikelets contribute to yield in sorghum and related grasses. The Plant Cell. 32(11):3500-3518. https://doi.org/10.1105/tpc.20.00424.

Analyzing mass spectrometry imaging data of 13C-labeled phospholipids in camelina sativa and thlaspi arvense (pennycress) embryos - (Peer Reviewed Journal)
Romsdahl, T.B., Kambhampati, S., Koley, S., Yadav, U.P., Alonso, A.P., Allen, D.K., Chapman, K.D. 2021. Analyzing mass spectrometry imaging data of 13C-labeled phospholipids in camelina sativa and thlaspi arvense (pennycress) embryos. Metabolites. 11(3). Article e148. https://doi.org/10.3390/metabo11030148.

Temporal changes in metabolism late in seed development affect biomass composition - (Peer Reviewed Journal)
Kambhampati, S., Aznar-Moreno, J.A., Bailey, S.R., Arp, J.J., Chu, K., Bilyeu, K.D., Durrett, T.P., Allen, D.K. 2021. Temporal changes in metabolism late in seed development affect biomass composition. Plant Physiology. 186(2):874-890. https://doi.org/10.1093/plphys/kiab116.

Quantification of acyl-acyl carrier proteins for fatty acid synthesis using LC-MS/MS - (Book / Chapter)
Jenkins, L.M., Nam, J., Evans, B.S., Allen, D.K. 2021. Quantification of acyl-acyl carrier proteins for fatty acid synthesis using LC-MS/MS. Methods in Molecular Biology. 2295:219-247. https://doi.org/10.1007/978-1-0716-1362-7_13.

Application of stable isotope tracing to elucidate metabolic dynamics during Yarrowia lipolytica a-ionone fermentation - (Peer Reviewed Journal)
Czajka, J.J., Kambhampati, S., Tang, Y.J., Wang, Y., Allen, D.K. 2020. Application of stable isotope tracing to elucidate metabolic dynamics during Yarrowia lipolytica a-ionone fermentation. iScience. 23(2):100854. https://doi.org/10.1016/j.isci.2020.100854.

On the inverse correlation of protein and oil: Examining the effects of altered central carbon metabolism on seed composition using soybean fast neutron mutants - (Peer Reviewed Journal)
Kambhampati, S., Aznar-Moreno, J.A., Hostetler, C., Caso, T., Bailey, S.R., Hubbard, A.H., Durrett, T.P., Allen, D.K. 2019. On the inverse correlation of protein and oil: Examining the effects of altered central carbon metabolism on seed composition using soybean fast neutron mutants. Metabolites. 10(1):18. https://doi.org/10.3390/metabo10010018.

Reorganization of acyl flux through the lipid metabolic network in oil-accumulating tobacco leaves - (Peer Reviewed Journal)
Zhou, X., Bhandari, S., Johnson, B.S., Kotapati, H., Allen, D.K., Vanhercke, T., Bates, P.D. 2020. Reorganization of acyl flux through the lipid metabolic network in oil-accumulating tobacco leaves. Plant Physiology. 182(2):739-755. https://doi.org/10.1104/pp.19.00667.

Tracing metabolic flux through time and space with isotope labeling experiments - (Peer Reviewed Journal)
Allen, D.K., Young, J.D. 2020. Tracing metabolic flux through time and space with isotope labeling experiments. Current Opinion in Biotechnology. 64:92-100. https://doi.org/10.1016/j.copbio.2019.11.003.

Accurate and efficient amino acid analysis for protein quantification using hydrophilic interaction chromatography coupled tandem mass spectrometry - (Peer Reviewed Journal)
Kambhampati, S., Li, J., Evans, B.S., Allen, D.K. 2019. Accurate and efficient amino acid analysis for protein quantification using hydrophilic interaction chromatography coupled tandem mass spectrometry. Plant Methods. 15:46. https://doi.org/10.1186/s13007-019-0430-z.

Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity - (Peer Reviewed Journal)
Abernathy, M., Czajka, J., Allen, D.K., Hill, N.C., Cameron, J.C., Tang, Y.J. 2019. Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity. Metabolic Engineering. 54:222-231. https://doi.org/10.1016/j.ymben.2019.04.010.