EMSL User Meeting 2023 | Agenda

Tuesday, Oct. 3 | Day 1

7:30 a.m. – Registration and badging

8:30 a.m. – Opening remarks

8:45 a.m. – Overview of EMSL, capabilities, and user program

SESSION 1 | Mapping metabolic processes of environmental systems with spatially resolved mass spectrometry and mass spectrometry imaging

Session co-chairs: Dusan Velickovic and Robert Stanley

9:15 a.m. – Session 1 – Keynote #1

• “Revealing the Intricacies of Organism-Environment Interactions using Spatial Metabolomics: A Path towards Understanding Adaptation and Acclimation”
  Malak Tfaily | Associate Professor | University of Arizona

9:55 a.m. – Session 1 – Contributing talk #1

• "A systems biology approach to reveal cell-type specific molecular responses to combined abiotic stresses in poplar"
  Vimal Kumar Balasubramanian | Biologist | EMSL

10:15 – Networking coffee break

10:30 a.m. – Session 1 – Contributing talk #2

• "Integrating multi-omic and isotopic tools to map nitrogen metabolism in the sorghum rhizosphere"
  Holly Andrews | Postdoctoral Research Associate | University of Arizona

10:50 a.m. – Session 1 – Contributing talk #3

• "A new in situ derivatization workflow for imaging carbonyls, phytohormones, and other hard to detect metabolites in environmental samples"
  Dusan Velickovic | Chemist | EMSL

11:10 a.m. – Session 1 – Keynote #2

• "In vivo isotope labeling of plant metabolites for mass spectrometry imaging"
  Young-Jin Lee | Professor of Chemistry | Iowa State University

11:50 a.m. – Lunch and flash talks

• Flash talks
   

  • "Demystifying the molecular mechanisms of glycoside hydrolases by glycoproteomics" 
    Stephanie Thibert | Postdoctoral Research Associate | Pacific Northwest National Laboratory

  • "Developing and validating SPE-ICP-MS method for arsenic speciation analysis in groundwater" 
    Andrew Oroke | PhD Student Researcher | Newcastle University 

  • "Solution NMR spectroscopy identifies unique backbone dynamics in the Xanthamonas sacchari bacterial expansin EXLX1"
    Garry Buchko | Chemist | Pacific Northwest National Laboratory 

12:50 p.m. - User Executive Committee session

SESSION 2 | Spatial and multimodal omics analysis of plant systems

Session co-chairs: Vimal Kumar Balasubramanian and Amir Ahkami

1:50 p.m. – Session 2 – Keynote #1

• “Enabling the Next Agricultural Revolution; Use of Single Cell Biology to Engineer Stronger, Healthier, and Better Crops”
  Marc Libault | Associate Professor | University of Nebraska-Lincoln

2:30 p.m. – Session 2 – Contributing talk #1

• "Using small multiples to visualize and interact with leafcutter ant fungal garden multi-omics data"
  Lisa Bramer | Data Scientist | Pacific Northwest National Laboratory

2:50 p.m. – Group photo

3:05 p.m. – Networking coffee break

3:20 p.m. – Session 2 – Contributing talk #2

• "Determining the topological arrangement of the macromolecular subunits using an integrative modeling approach: case of the chromatin remodeling complex INO80 from yeast S. cerevisiae"
  Jules Berlin Nde Kengne | PhD Student | University of Washington

3:40 p.m. – Session 2 – Contributing talk #3

• "Elucidating the molecular mechanisms of N-fixation by Populus Endophyte, Burkholderia vietnamiensis WPB"
  Jayde Aufrecht | Biologist | EMSL

4 p.m. – Session 2 – Keynote #2

• “Single-cell and spatial dissection of plant-microbe interactions”
  Tatsuya Nobori | Human Frontier Science Program Postdoctoral Fellow | Salk Institute

4:40 p.m. – Poster session and evening networking reception | Sponsored by Thermo Fisher Scientific

• Wine and light snacks served

Wednesday, Oct. 4 | Day 2

7:30 a.m. – Registration

SESSION 3 | Illuminating environmental processes using fluorescence microscopy tools

Session co-chairs: Dehong Hu and Lye Meng Markillie

8:30 a.m. – Session 3 – Keynote #1

• "EMSL enabled studies of plant receptor function"
  Gary Stacey | Curators Distinguished Professor of Plant Science & Technology | University of Missouri

9:10 a.m. – Session 3 – Contributing talk #1

• "Mapping microbial biogenic gas activity in peat soils at multiple scales of measurement using minimally invasive hydrogeophysical methods"
  Xavier Comas | Professor | Florida Atlantic University

9:30 a.m. – Session 3 – Keynote #2

• “Spatial Metallomics and Metabolomics to Understand Metabolic Pathways of Plants and Cells involved in Bioenergy Processes”
  Yi Lu | Robert J.V. Johnson-Welch Regents Chair in Chemistry | University of Texas at Austin

10:10 a.m. – Networking coffee break

10:25 p.m. – Session 3 – Contributing talk #2

• "Cellulose hydrolysis studied by infrared nanospectroscopy"
  Brian O’Callahan | Chemist | EMSL

10:45 a.m. – Session 3 – Contributing talk #3

• "Fine root chemical plasticity in response to nutrient heterogeneity impacts root decomposition"
  Vidya Suseela | Associate Professor | Clemson University

SESSION 4 | Imaging environmental processes using advanced light sources

Session co-chairs: Arunima Bhattacharjee and Tamas Varga

11:05 a.m. – Session 4 – Keynote #1

• "Deeper insights into calcium and potassium biogeochemical cycles from theory backed X-ray spectroscopy: An SSRL-EMSL collaboration"
  Ritimukta Sarangi | Senior scientist | SLAC National Accelerator Laboratory

11:45 a.m. – Session 4 – Contributing talk #1

• "RhizoGrid root cartography spatially maps plant metabolite-microbe interactions in the Sorghum rhizosphere"
  Pubudu Handakumbura | Biologist | EMSL

12:05 p.m. – Lunch, flash talks, and posters

• Flash talks: 

  • “Exploring the complexity of biological weathering with EMSL-based biogeochemical and mineralogical capabilities”
    Dragos Zaharescu | Assistant Project Scientist | University of California, Davis 

  • “Overcoming formaldehyde toxicity is critical to using lignin-derived aromatics” 
    Akorede Seriki | Research Assistant | University of Idaho 

1:20 p.m. – Session 4 – Contributing talk #2

• "Investigating the molecular processes controlling potassium translocation by fungi using synthetic soil habitats and synchrotron µ-XRF imaging"
  Jocelyn Richardson | Associate Scientist | SLAC National Accelerator Laboratory

1:40 p.m. – Session 4 – Keynote #2

• "High-resolution X-ray microscopy techniques for environmental studies and microbiology at the Advanced Photon Source"
  Si Chen | Physicist | Argonne National Laboratory

2:20 p.m. – Session 4 – Contributing talk #3

• "The use of multi-modal imaging for understanding plant-microbe interactions"
  Gyorgy Babnigg | Bioinformatician/Molecular Biologist | Argonne National Laboratory

2:40 p.m. – Networking coffee break

SESSION 5 | Revealing microscale and nanoscale environmental processes and interactions using electron microscopy

Session co-chairs: Jeremy Bougoure and Odeta Qafoku

2:55 p.m. – Session 5 – Keynote #1

• "Molecular to micron scale investigations of colloids to understand field scale elemental transport"
  Ken Kemner | Senior Physicist | Argonne National Laboratory

3:35 p.m. – Session 5 – Contributing talk #1

• "EMSL 1000 Fungal Proteins"
  James Evans | Chemist | EMSL

3:55 p.m. – Session 5 – Contributing talk #2

• "Nanoscale defects and melting behaviors of ice revealed at atomic resolution"
  Jingshan Du | Washington Research Foundation Postdoctoral Fellow | Pacific Northwest National Laboratory

4:15 p.m. – Session 5 – Contributing talk #3

• "Graph identification of proteins in tomograms – enhanced by machine learning"
  Chengxuan Li | PhD Student | University of Washington

4:35 p.m. – Session 5 – Keynote #2

• "Cross-scale analyses of soil development using EMSL's multimodal capabilities"
  Rebecca Lybrand | Assistant Professor | University of California, Davis

5:05 p.m. – Closing remarks

5:30 p.m. – Evening learning and networking session at Ste. Michelle Wine Estates WSU Wine Science Center

• Tour of WSU Wine Science Center laboratory facilities
• Wine and light refreshments served

Thursday, Oct. 5 | Day 3

Workshops | Part 1 (hosted in EMSL)

8 a.m. – Synthetic soil habitats/TerraForms (30 people max)

• Format: Presentation followed by in-lab activities.
• Required attire: Long pants, at least half sleeves, and close-toed shoes. Safety glasses will be provided as needed.
   
• Jayde Aufrecht | Biologist | EMSL
• Arunima Bhattacharjee | Chemist | EMSL
• Daisy Herrera | Postdoctoral Researcher | EMSL

8 a.m. – The potential of mass spectrometry imaging (40 people max)

• Format: Presentation, interactive discussion, and panel discussion.
   
• David Degnan | Data Scientist | PNNL
• Kevin Zemaitis | Postdoctoral Researcher | EMSL

10 a.m. – Networking coffee break (hosted in EMSL)

Workshops | Part 2 (hosted in EMSL)

10:15 a.m. – Lifecycle of an EMSL user proposal: How to hatch your next big idea (30 people max)

• Format: Presentation with audience engagement followed by two panels.
   
• Rick Washburn | Project Manager | EMSL
• Samantha Miller | Project Manager | EMSL
• Sarah Leichty | Project Manager | EMSL

10:15 a.m. – Sample prep for imaging (24 people max)

• Format: Presentation followed by in-lab activities.  
• Required attire: Long pants, at least half sleeves, and close-toed shoes.
   
• Vimal Kumar Balasubramanian | Biologist | EMSL
• Dusan Velickovic | Chemist | EMSL
• Robert Stanley | Postdoctoral Researcher | EMSL
• Dehong Hu | Chemist | EMSL
• Will Chrisler | Biomedical Scientist | PNNL
• Lye Meng Markillie | Biologist | EMSL
• Odeta Qafoku | Soil and Geochemist | EMSL

12:15 p.m. – Working lunch – reports, papers, roundtables (Discovery Hall)

2 p.m. – EMSL tour (begins in Discovery Hall)

3:30 p.m. – End of meeting

Poster presenters

Poster sessions take place at 4:40 p.m. on Oct. 3 and 12:05 p.m. on Oct. 4

• Arctic climate change feedbacks: Analyzing the impact of increasing temperatures on microbial community assembly in the Arctic Permafrost Peatlands
  Adeena Ahsan | Graduate Student | University of New Hampshire
   
• Evaluating post-fire changes in soil microbial communities involved in nitrogen cycling in the arctic tundra
  Alma Hernandez | Graduate Student | University of New Hampshire
   
• Elucidating the reaction pathways of veratrylglycero-β-guaiacyl ether degradation over metal-free solid acid catalyst with hydrogen
  Bin Yang | Professor | Washington State University
   
• Applying high-resolution microscopy to explore fungal-grain interactions and distribution across contrasting mineral types
  Cassandra Collins | University of California, Davis | Graduate student
   
• Electrochemically active biofilm in soil systems
  Christina Webster | Graduate Student | Washington State University
   
• Metabolic pathway mapping and molecular phenotyping of biological and environmental systems through EMSL SIP-NMR and SIP-MS metabolomic capabilities
  David Hoyt | Senior Research Scientist | EMSL
   
• Towards a general model for identifying particulate organic matter in X-ray microcomputed images of soil aggregates
  Devin Rippner | Research Soil Scientist | U.S. Department of Agriculture
   
• Investigating the molecular processes controlling potassium translocation by fungi using synthetic soil habitats and synchrotron µ-XRF imaging
  Jocelyn Richardson | Associate Scientist | SLAC National Accelerator Laboratory
   
• Root volatile organic compound signatures in a semiarid sorghum agroecosystem
  Linnea Honeker | Postdoctoral Research Associate | University of Arizona
   
• Using X-ray computed tomography and chemical extractions to examine mineral weathering in rock substrates deployed along a bioclimate gradient
  Madison Morris | Graduate Student | University of California, Davis
   
• Deep spatial metabolomics for confidential molecular identification in environmental samples
  Marija Velickovic | Chemist | EMSL
   
• Chemical composition, coordination, and stability of Ca (bicarbonate) organic associations in the presence of dissolving calcite
  Qian Zhao | Earth Scientist | EMSL
   
• Orthogonal mass spectrometry imaging techniques for more confident spatial identifications of small molecules
  Rosalie Chu | Chemist | EMSL
   
• Structural biology of plant cell wall biosynthetic enzymes
  Samantha Ziegler | Research Scientist | National Renewable Energy Laboratory
   
• Investigating the rate of horizontal gene transfer in the rhizosphere and environmental factors impacting it using fabricated ecosystems
  Priya Shweta | Postdoctoral Biologist | Lawrence Berkeley National Laboratory
   
• Soil porous microstructure control over soil organic matter mobility: the case of two arid soils
  Tamas Varga | Materials Scientist | EMSL