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Bhattacharjee A, Velickovic D, Richardson JA, Couvillion SP, Vandergrift GW, Qafoku O, Taylor MJ, Jansson JK, Hofmockel K, Anderton CR. Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot. mBio 2023; 14:e0095623. [PMID: 37655873 PMCID: PMC10653886 DOI: 10.1128/mbio.00956-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Fungal species are foundational members of soil ecosystems with vital contributions that support interspecies resource translocation. The minute details of these biogeochemical processes are poorly investigated. Here, we addressed this knowledge gap by probing fungal growth in a novel mineral-doped soil micromodel platform using spatially-resolved imaging methodologies. We found that fungi uptake K from K-rich minerals using organic acids exuded in a distance-dependent manner from a carbon-rich hotspot. While identification of specific mechanisms within soil remains challenging, our findings demonstrate the significance of reduced complexity platforms such as the mineral-doped micromodel in probing biogeochemical processes. These findings provide visualization into hyphal uptake and transport of mineral-derived nutrients in a resource-limited environment.
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Affiliation(s)
- Arunima Bhattacharjee
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jocelyn A. Richardson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sneha P. Couvillion
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory W. Vandergrift
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Odeta Qafoku
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael J. Taylor
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Janet K. Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten Hofmockel
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
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2
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Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU. A reference tissue atlas for the human kidney. Sci Adv 2022; 8:eabn4965. [PMID: 35675394 PMCID: PMC9176741 DOI: 10.1126/sciadv.abn4965] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 05/08/2023]
Abstract
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
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Affiliation(s)
- Jens Hansen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Sealfon
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | - Rajasree Menon
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Becky Steck
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kavya Anjani
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Samir Parikh
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Tara K. Sigdel
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Guanshi Zhang
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | | | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Dejan Dobi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Priyanka Rashmi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Edgar A. Otto
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Miguel Rivera
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Michael P. Rose
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Christopher R. Anderton
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John P. Shapiro
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Pamreddy
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Seth Winfree
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yuguang Xiong
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yongqun He
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ian H. de Boer
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Abhijit S. Naik
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kumar Sharma
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Minnie M. Sarwal
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Himmelfarb
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | - Brad Rovin
- Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Zoltan Laszik
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - M. Todd Valerius
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sanjay Jain
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
| | - Lisa M. Satlin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | | | - Ravi Iyengar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kidney Precision Medicine Project
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
- University of Michigan School of Medicine, Ann Arbor, MI, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- University of California San Francisco School of Medicine, San Francisco, CA, USA
- Ohio State University College of Medicine, Columbus, OH, USA
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
- European Molecular Biology Laboratory, Heidelberg, Germany
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Duke University School of Medicine, Durham, NC, USA
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
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3
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Wilson J, Bilbao A, Wang J, Liao YC, Velickovic D, Wojcik R, Passamonti M, Zhao R, Gargano AFG, Gerbasi VR, Pas̆a-Tolić L, Baker SE, Zhou M. Online Hydrophilic Interaction Chromatography (HILIC) Enhanced Top-Down Mass Spectrometry Characterization of the SARS-CoV-2 Spike Receptor-Binding Domain. Anal Chem 2022; 94:5909-5917. [PMID: 35380435 PMCID: PMC9003935 DOI: 10.1021/acs.analchem.2c00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 cellular infection is mediated by the heavily glycosylated spike protein. Recombinant versions of the spike protein and the receptor-binding domain (RBD) are necessary for seropositivity assays and can potentially serve as vaccines against viral infection. RBD plays key roles in the spike protein's structure and function, and thus, comprehensive characterization of recombinant RBD is critically important for biopharmaceutical applications. Liquid chromatography coupled to mass spectrometry has been widely used to characterize post-translational modifications in proteins, including glycosylation. Most studies of RBDs were performed at the proteolytic peptide (bottom-up proteomics) or released glycan level because of the technical challenges in resolving highly heterogeneous glycans at the intact protein level. Herein, we evaluated several online separation techniques: (1) C2 reverse-phase liquid chromatography (RPLC), (2) capillary zone electrophoresis (CZE), and (3) acrylamide-based monolithic hydrophilic interaction chromatography (HILIC) to separate intact recombinant RBDs with varying combinations of glycosylations (glycoforms) for top-down mass spectrometry (MS). Within the conditions we explored, the HILIC method was superior to RPLC and CZE at separating RBD glycoforms, which differ significantly in neutral glycan groups. In addition, our top-down analysis readily captured unexpected modifications (e.g., cysteinylation and N-terminal sequence variation) and low abundance, heavily glycosylated proteoforms that may be missed by using glycopeptide data alone. The HILIC top-down MS platform holds great potential in resolving heterogeneous glycoproteins for facile comparison of biosimilars in quality control applications.
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Affiliation(s)
- Jesse
W. Wilson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Aivett Bilbao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Juan Wang
- Biological
Sciences Division, Pacific Northwest National
Laboratories, 902 Battelle
Boulevard, Richland, Washington 99354, United States
| | - Yen-Chen Liao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Dusan Velickovic
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Roza Wojcik
- National
Security Directorate, Pacific Northwest
National Laboratories, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Marta Passamonti
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The
Netherlands
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Rui Zhao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Andrea F. G. Gargano
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The
Netherlands
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Vincent R. Gerbasi
- Biological
Sciences Division, Pacific Northwest National
Laboratories, 902 Battelle
Boulevard, Richland, Washington 99354, United States
| | - Ljiljana Pas̆a-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Scott E. Baker
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
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4
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Honeker LK, Hildebrand GA, Fudyma JD, Daber LE, Hoyt D, Flowers SE, Gil-Loaiza J, Kübert A, Bamberger I, Anderton CR, Cliff J, Leichty S, AminiTabrizi R, Kreuzwieser J, Shi L, Bai X, Velickovic D, Dippold MA, Ladd SN, Werner C, Meredith LK, Tfaily MM. Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques. Environ Sci Technol 2022; 56:2021-2032. [PMID: 35048708 DOI: 10.1021/acs.est.1c06772] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific 13C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.
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Affiliation(s)
- Linnea K Honeker
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Biosphere 2, University of Arizona, 32540 South Biosphere Road, Oracle, Arizona 85739, United States
| | - Gina A Hildebrand
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - L Erik Daber
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - David Hoyt
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Sarah E Flowers
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, 1064 East Lowell Sreet, Tucson, Arizona 85721, United States
| | - Angelika Kübert
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Ines Bamberger
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Christopher R Anderton
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - John Cliff
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Sarah Leichty
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Roya AminiTabrizi
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - Jürgen Kreuzwieser
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Lingling Shi
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Xuejuan Bai
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, 712100 Shaanxi, China
| | - Dusan Velickovic
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - S Nemiah Ladd
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Christiane Werner
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Laura K Meredith
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Biosphere 2, University of Arizona, 32540 South Biosphere Road, Oracle, Arizona 85739, United States
- School of Natural Resources and the Environment, University of Arizona, 1064 East Lowell Sreet, Tucson, Arizona 85721, United States
| | - Malak M Tfaily
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
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5
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Chae S, Xu Y, Yi R, Lim HS, Velickovic D, Li X, Li Q, Wang C, Zhang JG. A Micrometer-Sized Silicon/Carbon Composite Anode Synthesized by Impregnation of Petroleum Pitch in Nanoporous Silicon. Adv Mater 2021; 33:e2103095. [PMID: 34398477 DOI: 10.1002/adma.202103095] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Porous silicon (Si)/carbon nanocomposites have been extensively explored as a promising anode material for high-energy lithium (Li)-ion batteries (LIBs). However, shrinking of the pores and sintering of Si in the nanoporous structure during fabrication often diminishes the full benefits of nanoporous Si. Herein, a scalable method is reported to preserve the porous Si nanostructure by impregnating petroleum pitch inside of porous Si before high-temperature treatment. The resulting micrometer-sized Si/C composite maintains a desired porosity to accommodate large volume change and high conductivity to facilitate charge transfer. It also forms a stable surface coating that limits the penetration of electrolyte into nanoporous Si and minimizes the side reaction between electrolyte and Si during cycling and storage. A Si-based anode with 80% of pitch-derived carbon/nanoporous Si enables very stable cycling of a Si||Li(Ni0.5Co0.2Mn0.3)O2 (NMC532) battery (80% capacity retention after 450 cycles). It also leads to low swelling in both particle and electrode levels required for the next generation of high-energy LIBs. The process also can be used to preserve the porous structure of other nanoporous materials that need to be treated at high temperatures.
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Affiliation(s)
- Sujong Chae
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Industrial Chemistry, Pukyong National University, Busan, 48513, Republic of Korea
| | - Yaobin Xu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Ran Yi
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Hyung-Seok Lim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Dusan Velickovic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Xiaolin Li
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Qiuyan Li
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chongmin Wang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Ji-Guang Zhang
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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6
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Lukowski JK, Pamreddy A, Velickovic D, Zhang G, Pasa-Tolic L, Alexandrov T, Sharma K, Anderton CR. Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility. J Am Soc Mass Spectrom 2020; 31:2538-2546. [PMID: 32897710 PMCID: PMC8162764 DOI: 10.1021/jasms.0c00256] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. We sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at -80 °C, vacuumed sealed and stored at -80 °C, with matrix preapplied before storage at -80 °C, under a nitrogen atmosphere and stored at -80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at -80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.
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Affiliation(s)
- Jessica K Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Annapurna Pamreddy
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
| | - Dusan Velickovic
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Guanshi Zhang
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
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7
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Angerer TB, Velickovic D, Nicora CD, Kyle JE, Graham DJ, Anderton C, Gamble LJ. Exploiting the Semidestructive Nature of Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry Imaging for Simultaneous Localization and Confident Lipid Annotations. Anal Chem 2019; 91:15073-15080. [PMID: 31659904 PMCID: PMC7430256 DOI: 10.1021/acs.analchem.9b03763] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lipids have been recognized as key players in cell signaling and disease. Information on their location and distribution within a biological system, under varying conditions, is necessary to understand the contributions of different lipid species to an altered phenotype. Imaging mass spectrometry techniques, such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and matrix-assisted laser desorption/ionization (MALDI), are capable of revealing global lipid distributions in tissues in an untargeted fashion. However, to confidently identify the species present in a sample, orthogonal analyses like tandem MS (MS/MS) are often required. This can be accomplished by bulk sample analysis with liquid chromatography (LC)-MS/MS, which can provide confident lipid identifications, at the expense of losing location-specific information. Here, using planarian flatworms as a model system, we demonstrate that imaging gas cluster ion beam (GCIB)-ToF-SIMS has the unique capability to simultaneously detect, identify, and image lipid species with subcellular resolution in tissue sections. The parallel detection of both, intact lipids and their respective fragments, allows for unique identification of some species without the need of performing an additional orthogonal MS/MS analysis. This was accomplished by correlating intact lipid and associated fragment SIMS images. The lipid assignments, respective fragment identities, and locations gathered from ToF-SIMS data were confirmed via LC-MS/MS on lipid extracts and ultrahigh mass resolution MALDI-MS imaging. Together, these data show that the semidestructive nature of ToF-SIMS can be utilized advantageously to enable both confident molecular annotations and to determine the locations of species within a biological sample.
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Affiliation(s)
- Tina B. Angerer
- NESACBIO, University of Washington, Seattle, Washington 98195
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
| | - Dusan Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Carrie D. Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Jennifer E. Kyle
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Daniel J. Graham
- NESACBIO, University of Washington, Seattle, Washington 98195
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
| | - Christopher Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Lara J. Gamble
- NESACBIO, University of Washington, Seattle, Washington 98195
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
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Prlainovic N, Bezbradica D, Knezevic-Jugovic Z, Velickovic D, Mijin D. Enzymatic synthesis of vitamin B6 precursor. JSCS 2013. [DOI: 10.2298/jsc130322050p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
3-Cyano-4-ethoxymethyl-6-methyl-2-pyridone is an important precursor in the
synthesis of vitamin B6, obtained in the addition reaction between
2-cyanoacetamide and 1-ethoxy-2,4-pentanedione catalyzed by lipase from
Candida rugosa (triacylglycerol ester hydrolases, EC 3.1.1.3). This work
shows new experimental data and mathematical modeling of lipase catalyzed
synthesis of 3-cyano-4-ethoxymethyl-6-methyl-2-pyridone, starting from
1-ethoxy-2,4-pentanedione and 2-cyanoacetamide. Kinetic measurements were
done at 50 oC with enzyme concentration of 1.2 % w/v. Experimental results
were fitted with two kinetic models: the ordered bi-ter and ping-pong bi-ter
model, and the initial rates of the reaction were found to correlate best
with a ping-pong bi-ter mechanism with inhibition by 2-cyanoacetamide.
Obtained specificity constants indicated that lipase from C. rugosa had
higher affinity towards 1-ethoxy-2,4-pentanedione and less bulky substrates.
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Affiliation(s)
| | | | | | | | - Dusan Mijin
- Faculty of Technology and Metallurgy, Belgrade
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Bjelovic M, Pesko P, Micev M, Todorovic V, Stojakov D, Sabljak P, Simic A, Ebrahimi K, Velickovic D, Spica B. The significance of lymphonodal micrometastasis in the patients with gastric adenocarcinoma. ACTA ACUST UNITED AC 2006; 52:21-4. [PMID: 16812989 DOI: 10.2298/aci0503021b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Micrometastasis is defined as microscopical deposit of malignant cells, less than 2mm in diameter, separated from the primary tumor. This does not include discontinous growth in peritumoral region, but include microinolvement of regional lymph nodes. The literature on micrometastases, with special resperct to nodal micrometastasis, and their implications in gastric adenocarcinoma have been reviewed. Immunohistochemical detection offer the best accuracy for detection of nodal micrometastasis. Molecular techniques are more sensitive than method of immunohistochemical detection, but methods are compromised with false positive results caused by various sources of biological contamination. It is more than obvious that there is no definite agreement neither about risk factors, nor definitive clinical significance of micrometastatic node involvement in the patients with gastric adenocarcinoma. At present, the role of occult lymph node involvement proved its significance in two major fields: defining criteria for limited surgical dissection in the patients with early (sm) carcinoma in respect to detection of micrometastatic tissue in sentinel lymph node, and distinguishing the category of pN0 (Mi+) patients with potential benefit of postoperative adjuvant therapy.
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Affiliation(s)
- M Bjelovic
- Department of Esophagogastric Surgery, Belgrade
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