Advanced Bioimaging Laboratory

2021

Anderson, C.M., Mattoon, E.M., Zhang, N., Becker, E., McHargue, W., Yang, J., Patel, D., Dautermann, O., McAdam, S.A.M., Tarin, T., Pathak, S., Avenson, T.J., Berry, J., Braud, M., Niyogi, K.K., Wilson, M., Nusinow, D.A., Vargas, R., Czymmek, K.J., Eveland, A.L. and Zhang, R. (2021) High light and high temperature reduce photosynthesis via different mechanisms in the c₄ model Setaria viridis. bioRxiv, 431694. doi:10.1101/2021.02.20.431694

 

Cox, K.L., Manchego, J., Meyers, B.C., Czymmek, K.J. and Harkess, A. (2021) Automated imaging of duckweed growth and development. bioRxiv, 453240. doi:10.1101/2021.07.21.453240

 

Gillman, J.D., Chebrolu, K. and Smith, J.R. (2021) Quantitative trait locus mapping for resistance to heat-induced seed degradation and low seed phytic acid in soybean. Crop Sci 61, 2023-2035. doi:10.1002/csc2.20419

 

Gurazada, S.G.R., Cox, K.L., Czymmek, K.J. and Meyers, B.C. (2021) Space: the final frontier - achieving single-cell, spatially resolved transcriptomics in plants. Emerg Top Life Sci 5, 179-188. doi:10.1042/etls20200274

 

Harkess, A., McLoughlin, F., Bilkey, N., Elliott, K., Emenecker, R., Mattoon, E., Miller, K., Czymmek, K., Vierstra, R., Meyers, B.C. and Michael, T.P. (2021) Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundances of chloroplastic proteins favoring energy production. J Exp Bot 72, 2491-2500. doi:10.1101/2020.01.23.909457

 

Hung, Y.-H. and Slotkin, R.K. (2021) The initiation of RNA interference (RNAi) in plants. Curr Opin Plant Biol 61, 102014. doi:10.1016/j.pbi.2021.102014

 

Kim, H.S., Kim, J.E., Hwangbo, A., Akerboom, J., Looger, L.L., Duncan, R., Son, H., Czymmek, K.J. and Kang, S. (2021) Evaluation of multi-color genetically encoded Ca(2+) indicators in filamentous fungi. Fungal Genet Biol 149, 103540. doi:10.1016/j.fgb.2021.103540

 

Romsdahl, T.B., Kambhampati, S., Koley, S., Yadav, U.P., Alonso, A.P., Allen, D.K. and Chapman, K.D. (2021) Analyzing mass spectrometry imaging data of (13)C-labeled phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) embryos. Metabolites 11, 148. doi:10.3390/metabo11030148

 

Zhang, N., Mattoon, E.M., McHargue, W., Venn, B., Zimmer, D., Pecani, K., Jeong, J., Anderson, C.M., Chen, C., Berry, J.C., Xia, M., Tzeng, S.-C., Becker, E., Pazouki, L., Evans, B., Cross, F., Cheng, J., Czymmek, K.J., Schroda, M., Mühlhaus, T. and Zhang, R. (2021) Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. bioRxiv, 456552. doi:10.1101/2021.08.17.456552

 

2020

AuBuchon-Elder, T., Coneva, V., Goad, D.M., Jenkins, L.M., Yu, Y., Allen, D.K. and Kellogg, E.A. (2020) Sterile spikelets contribute to yield in sorghum and related grasses. Pl Cell 32, 3500-3518. doi:10.1105/tpc.20.00424

 

Bélanger, S., Pokhrel, S., Czymmek, K.J. and Meyers, B.C. (2020) Pre-meiotic, 24-nucleotide reproductive phasiRNAs are abundant in anthers of wheat and barley but not rice and maize. Plant Physiol 184, 1407-1423. doi:10.1104/pp.20.00816

 

Chu, K., Jenkins, L.M., Bailey, S.R., Kambhampati, S., Koley, S., Foley, K., Arp, J.J., Czymmek, K.J., Bates, P.D. and Allen, D.K. (2020) Shifting carbon flux from non-transient starch to lipid allows oil accumulation in transgenic tobacco leaves. bioRxiv, 098632. doi:10.1101/2020.05.15.098632

 

Czymmek, K., Sawant, A., Goodman, K., Pennington, J., Pedersen, P., Hoon, M. and Otegui, M.S. (2020) Imaging plant cells by high-pressure freezing and serial block-face scanning electron microscopy. Methods Mol Biol 2177, 69-81. doi:10.1007/978-1-0716-0767-1_7

 

Czymmek, K., Duncan, K., Zhang, N. and Zhang, R. (2020) Strategies for optimizing heavy metal staining in freeze-substituted resin embedded plants samples for electron and x-ray microscopy. Microsc Microanal 26, 142-143. doi:10.1017/S1431927620013550

 

Duncan, K.E., Czymmek, K.J., Jiang, N., Thies, A.C. and Topp, C.N. (2020) X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs. bioRxiv, 423480. doi:10.1101/2020.12.18.423480

 

Liu, Z., Nguyen, Q.P.H., Nanjundappa, R., Delgehyr, N., Megherbi, A., Doherty, R., Thompson, J., Jackson, C., Albulescu, A., Heng, Y.M., Lucas, J.S., Dell, S.D., Meunier, A., Czymmek, K., Mahjoub, M.R. and Mennella, V. (2020) Super-resolution microscopy and FIB-SEM imaging reveal parental centriole-derived, hybrid cilium in mammalian multiciliated cells. Devel Cell 55, 224-+. doi:10.1016/j.devcel.2020.09.016

 

Negi, S., Perrine, Z., Friedland, N., Kumar, A., Tokutsu, R., Minagawa, J., Berg, H., Barry, A.N., Govindjee, G. and Sayre, R. (2020) Light-regulation of light harvesting antenna size substantially enhances photosynthetic efficiency and biomass yield in green algae. Plant J 103, 584-603. doi:10.1111/tpj.14751

 

Prunet, N. and Duncan, K. (2020) Imaging flowers: a guide to current microscopy and tomography techniques to study flower development. J Exp Bot 71, 2898-2909. doi:10.1093/jxb/eraa094

 

Velivelli, S.L.S., Czymmek, K.J., Li, H., Shaw, J.B., Buchko, G.W. and Shah, D.M. (2020) Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection. Proc Natl Acad Sci U S A 117, 16043-16054. doi:10.1073/pnas.2003526117

 

Wu, G.H., Mitchell, P.G., Galaz-Montoya, J.G., Hecksel, C.W., Sontag, E.M., Gangadharan, V., Marshman, J., Mankus, D., Bisher, M.E., Lytton-Jean, A.K.R., Frydman, J., Czymmek, K. and Chiu, W. (2020) Multi-scale 3D cryo-correlative microscopy for vitrified cells. Structure 28, 1231-1237. doi:10.1016/j.str.2020.07.017

 

2019

Augustin, M.M., Augustin, J.M., Brock, J.R. and Kutchan, T.M. (2019) Enzyme morphinan N-demethylase for more sustainable opiate processing. Nature Sustain 2, 465-474. doi:10.1038/s41893-019-0302-6

 

Ivanov, S., Austin, J., 2nd, Berg, R.H. and Harrison, M.J. (2019) Extensive membrane systems at the host-arbuscular mycorrhizal fungus interface. Nature Plants 5, 194-203. doi:10.1038/s41477-019-0364-5

 

Li, H., Velivelli, S.L.S. and Shah, D.M. (2019) Antifungal potency and modes of action of a novel olive tree defensin against closely related ascomycete fungal pathogens. Mol Plant Mic In 32, 1649-1664. doi:10.1094/mpmi-08-19-0224-r

 

Liberton, M., Bandyopadhyay, A. and Pakrasi, H.B. (2019) Enhanced nitrogen fixation in a glgX-deficient strain of Cyanothece sp. Strain ATCX 51142, a unicellular nitrogen-fixing cyanobacterium. Appl Environ Microbiol 85, e02887-02818. doi:10.1128/aem.02887-18

 

Singh, R., Low, E.-T.L., Ooi, L.C.-L., Ong-Abdullah, M., Ting, N.-C., Nookiah, R., Ithnin, M., Marjuni, M., Mustaffa, S., Yaakub, Z., Amiruddin, M.D., Manaf, M.A.A., Chan, K.-L., Halim, M.A.A., Sanusi, N.S.N.M., Lakey, N., Sachdeva, M., Bacher, B., Garner, P.A., MacDonald, J.D., Smith, S.W., Wischmeyer, C., Budiman, M.A., Beil, M., Stroff, C., Reed, J., Van Brunt, A., Berg, H., Ordway, J.M. and Sambanthamurthi, R. (2019) Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles. New Phytol. doi:10.1111/nph.16387

 

Teisher, J. K., McKain, M. R., Schaal, B. A., and Kellogg, E. A. (2019) Plastome phylogenetics of tribe Eriachneae and evolution of C4 photosynthesis in subfamily Micrairoideae (Poaceae). Systematic Botany 44: 32-40.  doi: 10.1600/036364419X697877

 

Yu, Y., Hu, H., Doust, A. N., and Kellogg, E. A. (2019) Divergent gene expression networks underlie morphological diversity of abscission zone development in grasses (Poaceae).  New Phytologist: early view. doi.org/10.1111/nph.16087

 

Yuan, S., Kim, S.-C., Deng, X., Hong, Y. and Wang, X. (2019) Diacylglycerol kinase and associated lipid mediators modulate rice root architecture. New Phytol 223, 261-276. doi:10.1111/nph.15801

 

2018

Ganguly, A., DeMott, L., Zhu, C., McClosky, D.D., Anderson, C.T. and Dixit, R. (2018) Importin-β directly regulates the motor activity and turnover of a kinesin-4. Dev Cell 44, 642-651.e645. doi:10.1016/j.devcel.2018.01.027

 

Teng, C., Zhang, H., Hammond, R., Huang, K., Meyers, B. and Walbot, V. (2018) Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. bioRxiv, 498410. doi:10.1101/498410

 

Velivelli, S.L.S., Islam, K.T., Hobson, E. and Shah, D.M. (2018) Modes of action of a bi-domain plant defensin MtDef5 against a bacterial pathogen Xanthomonas campestris. Front Microbiol 9. doi:10.3389/fmicb.2018.00934

 

Zhu, C., Yang, J., Box, M. C., Kellogg, E. A., and Eveland, A. L. (2018) A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics. Frontiers in Plant Science 9: 1309. doi: 10.3389/fpls.2018.01309.

 

Huang, P., Jiang, H., Barry, K., Jenkins, J., Schmutz, J., Box, M. S., Zhu, C., Kellogg, E. A., and Brutnell, T. P.  (2017) The sparse panicle1 gene of Setaria viridis and maize is required for inflorescence branch development and root agravitropism. Nature Plants 3: 17054.  doi: 10.1038/nplants.2017.54 | www.nature.com/natureplants

In order to track our impact and productivity, the ABL appreciates acknowledgment in your publications and poster presentations as follows: 

 

Generic Acknowledgment

”We wish to thank (staff name here) from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Donald Danforth Plant Science Center for support with (imaging support provided)…”

 

Equipment Funding Acknowledgment

All publications using instruments in the Advanced Bioimaging Laboratory must include the following statement in the acknowledgments if this equipment was used in their published work:

• ZEISS Elyra 7 Super-Resolution Microscope
  “We acknowledge imaging support from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Danforth Plant Science Center and usage of the ZEISS Elyra 7 Super-Resolution Microscope acquired through an NSF Major Research Instrumentation grant (DBI-2018962).”

• ThermoFisher Scientific Talos L120C Transmission Electron Microscope  (TEM)
  “We acknowledge imaging support from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Danforth Plant Science Center and usage of the ThermoFisher Scientific Talos L120C TEM acquired through generous donor support to the Donald Danforth Plant Science Center.”

• Leica SP8-X
  “We acknowledge imaging support from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Danforth Plant Science Center and usage of the Leica SP8-X confocal microscope acquired through an NSF Major Research Instrumentation grant
  (DBI-1337680).”

• Zeiss PALM Laser Microdissection System
  “We acknowledge imaging support from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Danforth Plant Science Center and usage of the Zeiss PALM Laser Microdissection System acquired through an NSF Major Research Instrumentation grant (DBI-0421407).”

• ThermoFisher Scientific Hydra Plasma FIB  (SEM)“
  "We acknowledge imaging support from the Advanced Bioimaging Laboratory (RRID:SCR_018951) at the Danforth Plant Science Center and usage of the ThermoFisher Scientific Hydra Plasma FIBSEM acquired through generous donor support to the Donald Danforth Plant Science Center..”

If contributions go beyond our standard microscopy fee-for-service support, including significant intellectual contribution and/or manuscript preparation, the ABL support staff should be considered for co-authorship.

 

Core facilities must charge for services rendered according to cost accounting practices set up at each institution. Charging for services does not preclude authorship on manuscripts provided the Core laboratory individual has contributed to the research in a substantial way.  If authorship is anticipated, it is preferably established at the beginning of the project so that both the customer and the Core researcher are cognizant of each other’s criteria.

If contributions go beyond our standard microscopy fee-for-service support and include significant intellectual contribution and/or manuscript preparation, the ABL support staff should be considered for co-authorship.

 

Core facilities must charge for services rendered according to cost accounting practices set up at each institution. Charging for services does not preclude authorship on manuscripts provided the Core laboratory individual has contributed to the research in a substantial way.  If authorship is anticipated, it is preferably established at the beginning of the project so that both the customer and the Core researcher are cognizant of each other’s criteria.

 

Important reasons for acknowledging contributions from core facilities in publications, by co-authorship or by formal mention in the acknowledgments section, include:

1. Core facility personnel are scientists. When they make a substantial intellectual and/or experimental contribution to a publication they deserve to be acknowledged just as any other co-author.
2. The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.

 

Activities for which authorship are recommended:

• Author should make substantive contributions to the project, such as:
  • Conception, design of project, critical input, or original ideas
  • Acquisition of data, analysis and interpretation, beyond routine practices
  • Draft the article or revise it critically for intellectual content
  • Write a portion of the paper (not just materials and methods section)
  • Intellectual contribution
  • Final authority for the approval of article

• Each author should have participated enough to accept responsibility for the content of the manuscript.

 

The following activities do not represent intellectual contributions to a project and would not constitute authorship:

• Providing funding (department chair who has no intellectual input)
• Collection of data (technical skill but not involved in interpretation of data)
• General supervision of research group, but no intellectual input into the project

 

All contributors that do not meet the criteria of authorship should be recognized in the acknowledgments section, for example:

• Paid technical help
• Writing assistance
• Financial and material support
• Scientific advice

 

Two examples are pertinent: (from Robert A. Day: How to Write and Publish a Scientific Paper, 5th Edition)

 

Example 1: Scientist A designs the experiments, and tells Technician B exactly how to do the experiments. If the experiments work and a new discovery is made and a manuscript results, Scientist A is the sole author and Technician B is recognized in the acknowledgements section.

 

Example 2: Scientist A designs the experiments, Technician B carries them out but they do not work. Technician B suggests some changes to the protocol, the experiments then work because of the changes and a discovery results. Scientist A and Technician B are now both authors.