2018 RC-SIRM Symposium and Workshop


Overall Description

Established in 2013, the University of Kentucky's NIH-funded RC-SIRM: Resource Center for Stable Isotope-Resolved Metabolomics presents its 12-day "gloves on and gloves off" Workshop , Monday, July 23 through Friday, August 3, 2018 and its one day Metabolomics Symposium on Monday, July 30, 2018. RC-SIRM is one of six NIH Regional Comprehensive Metabolomics Resource Cores supported by the NIH Common Fund. Attendees of the Workshop will gain working knowledge in the application of SIRM to fundamental biochemistry research in the life sciences and bench-to-bedside translational research.
  • ALL EVENTS will occur in the Lee Todd Jr. Building at 789 S. Limestone St. (formerly the BioPharmacy Building) on the campus of the University of Kentucky.
  • Workshop attendees are asked to arrive and check in to their on-campus lodging on SUNDAY, JULY 22, 2018.

Workshop - Stable Isotope-Resolved Metabolomics: Experimental design, methods, and data analysis

The 12-day workshop is appropriate for graduate students, technicians, post-docs, and faculty who wish to integrate stable isotope-enabled studies of metabolism into their experimental design.
  • Attendees of the Workshop will gain working knowledge in the application of SIRM to fundamental biochemistry research in the life sciences and bench-to-bedside translational research.
  • The hands-on Workshop is limited to 20 participants with relevant background:
    • Applications for the Workshop participation will be accepted until July 16, 2018.
    • Workshop registration is $3,750 and includes the Symposium and on-campus lodging.
  • Some scholarships are available to offset travel costs for students and post-doctoral fellows whose poster abstracts demonstrate excellence in the science of SIRM.
  • Stable isotope tracer-based biological experiments
  • Cell and tissue processing, polar and non-polar metabolite extraction, and preparation for MS and NMR analysis
  • Data acquisition with the Center¬ís Mass and NMR Spectrometers
  • Large-scale analysis of MS and NMR data for metabolites and their stable isotope labeling patterns

2018 Workshop Agenda and Schedule

Sunday July 22, 2018

Afternoon
  • Arrive in Lexington, KY
  • 4:30 – 6:30: Meet and Greet with lab staff, PI’s and workshop participants
    • 789 South Limestone Street, Lee T. Todd Jr Building Atrium
Day 1: Monday July 23, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building.
    • Continental breakfast will be provided
    • Orientation-Provide Overview of Week.
    • Present Laboratory Rules and OSHA Rules and Personal Protective Equipment.
    • Assignment of participants into two Groups
  • 9:00 – 9:30: Overview of learning goals and expected workshop outcomes.
    • Led by Dr. Teresa Fan, 570 Lee T. Todd Jr Building
  • 9:30-10:00: General Introduction to SIRM -
    • Led by Dr. Teresa Fan, Room 570 Lee T. Todd Jr. Building
  • 10:00 – 11:00: Introduction to SIRM and Panc-1 cells and experimental background, questions, and design
    • Led by Dr. Teresa Fan, Room 570 Lee T. Todd Jr. Building
  • 11:00 – 12:00: Overview of experimental design: statistical considerations
    • Led by Dr. Hunter Moseley, Room 570 Lee T. Todd Jr. Building

Afternoon
  • 12:00 –1:00: Lunch
    • Room 570 Lee T. Todd Jr. Building
      • Lunch will be provided
  • 1:00 – 2:00: Instruction on calculating formulae for enriched media and treatments
    • Led by Dr. Teresa Fan, Room 570 Lee T. Todd Jr. Building
  • 2:00 – 3:00: Introduction and Demonstration of metadata spreadsheet for tracer experiment
    • Led by Teresa Cassel, Room 570 Lee T. Todd Jr. Building
  • 3:00 – 3:30: Demonstration of cell culture tracer experiment
    • Led by Dr. Teresa Fan
  • 3:30 – 4:00: Demonstration of tissue grinding and methanol rinse/tissue quenching for extraction
    • Led by Teresa Cassel
  • 4:00 – 4:30: Guided practice of metadata entry into template and recap/questions
    • Led by Dr. Teresa Fan, 570 Lee T. Todd Jr. Building
  • 4:30 – 5:30: Demonstration of course medium sampling
    • Led by Dr. Teresa Fan
Day 2: Tuesday July 24, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building
    • Continental Breakfast will be provided
    • Watch the quenching video tutorial
  • 9:00 – 12:00: Step by step demonstration and participant practice of cell culture harvest and quenching
    • Led by Dr. Teresa Fan

Afternoon
  • 12:00 – 1:00: Lunch
    • Room 570 Lee T. Todd Jr. Building
      • Lunch will be provided
    • Watch the extraction tutorial video
  • 1:00 – 4:30: Step by step demonstration and participant practice of polar/non-polar extraction of cell lysates
    • Led by Dr. Teresa Fan
  • 4:30 – 5:30: Step by step demonstration and participant practice of polar fraction aliquot and lipid reconstitution
    • Led by Dr. Teresa Fan
  • 5:30 – 6:15: Guided practice of metadata entry into template and recap/questions
    • Led by Dr. Teresa Fan
Day 3: Wednesday July 25, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570, Lee T. Todd Jr. Building
    • Continental breakfast will be provided
    • Discussion of lyophilization theory and practice
      • Led by Dr. Richard Higashi
  • 9:00 – 10:30: Step by step demonstration and participant practice of protein extraction
    • Led by Dr. Teresa Fan
  • 10:30 – 10:45: Break
  • 10:45 – 12:30: Demonstration of protein extract dilution determination for BCA analysis
    • Led by Dr. Teresa Fan

Afternoon
  • 12:30 – 1:30: Lunch - Room 570 Lee T. Todd Jr. Building
    • Lunch will be provided
    • Participants will be oriented to the metadata spreadsheet for their solo practice plates - Led by Teresa Cassel
  • 1:30 – 3:00: Step-by-step demonstration and participant practice of protein quantification by BCA
    • Led by Dr. Teresa Fan
  • 3:00 – 3:15: Break
  • 3:15 – 4:30: Step-by-step demonstration and participant practice of media extraction
    • Led by Dr. Teresa Fan
  • 4:30 – 5:00: Demonstration of lyophilization of polar fractions
    • Supervised by Dr. Richard Higashi
  • 5:00 – 6:00: Guided practice of metadata entry into template and calculation of protein concentration from BCA data
    • Led by Dr. Teresa Fan, Room 570 Lee T. Todd Jr. Building
Day 4: Thursday July 26, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
    • General introduction to statistics - Led by Dr. Hunter Moseley
  • 9:00 – 10:00: Practical applications of statistics - Led by Dr. Hunter Moseley
  • 10:00 - 11:30:Participants solo practice of cell culture harvest and quenching

Afternoon
  • 11:30 – 12:30: Lunch is provided.
    • Room 570 -Lee T. Todd Jr. Building
  • 12:30 - 2:30: Participants solo practice of polar non-polar cell extraction
  • 2:30 - 5:30: Overview NMR data analysis: isotopomers and their quantification
    • Led by Dr. Andrew Lane,
      • Room 570 Lee T. Todd Jr. Building
Day 5: Friday July 27, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 -Lee T. Todd Jr. Building
    • Continental breakfast will be provided
  • 9:00 – 12:30: Step by step demonstration and participant practice of NMR data analysis –
    • Led by Dr. Teresa Fan; Room 570 Lee T. Todd Jr. Building

Afternoon
  • 12:30 – 1:30: Lunch - Room 570, Lee T. Todd Jr. Building Lunch is provided
  • 1:30 – 4:30: Independent practice NMR data analysis
  • 4:30 – 5:00: Break
  • 5:00 – 6:00: Presentation from data processing to biochemical interpretation: Part I
    • Led by Dr. Teresa Fan; Room 570 Lee T. Todd Jr. Building
  • 6:00 – 6:30: Recap and Questions
Day 6: Saturday July 28, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
    • Overview of targeted and untargeted chromatography FTMS
      • Led by Dr. Richard Higashi
  • 9:00 – 12:00: Overview of IC-FTMS and its data processing. Curation demonstration and participant practice of IC-FTMS targeted data processing -

Afternoon
  • 12:00 – 1:00: Lunch - Room 570 Lee T. Todd Jr. Building Lunch is provided
  • 1:00 – 3:00: Participants solo practice of protein extraction
  • 3:00 – 5:30: Quantification demonstartion and participant practice of IC-FTMS targeted data processing - Participants practice IC-FTMS data processing.
    • Dr. Jessica Kele Arruda Macedo
  • 5:30 – 6:30: Optional practice time for NMR or IC-FTMS data processing
Day 7: Sunday July 29, 2018

  • 9:30 – 10:00 Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
  • 10:00 – 12:00 Roundtable discussion regarding metabolomics
    Afternoon
  • 12:00 – 1:00 Lunch - Room 570 Lee T. Todd Jr. Building Lunch is provided
    Solo practice of metadata entry into template – Complete solo metadata file
    (Provide participants with polar aliquot and BCA data)
  • 1:00 – 2:00 Introduce participants to pathway analysis assignment. Provide complete SIRM data set from experiment using a PC suppressor. Led by Dr. Teresa Fan, 570 Lee T. Todd Jr. Building
  • 2:00 – 4:00 General introduction to statistics Practical applications of statistics – Led by Dr. Hunter Moseley
    570 Lee T. Todd Jr. Building
Day 8: Monday July 30, 2018 – Symposium
  • Registration begins at 8:00 am
Day 9: Tuesday July 31, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
    • Overview of targeted and untargeted direct infusion FTMS: example of “shotgun” lipids analysis and its data processing requirements - Led by Dr. Richard Higashi
  • 9:00 – 12:00: Participants practice targeted NMR or pathway analysis, depending on individual previous progress.

Afternoon
  • 12:00 – 1:00: Lunch - Room 570 Lee T. Todd Jr. Building Lunch is provided
  • 1:00 – 3:30: Participants practice pathway analysis
  • 3:30 – 4:00: Break
  • 4:00 – 5:30: Presentation from data processing to biochemical interpretation: Part II – Led by Dr. Teresa Fan
  • 5:30 – 6:30: Guided practice of metadata entry into template – Led by Dr. Teresa Fan Room 570 -Lee T. Todd Jr. Building
    • (Provide participants with polar aliquot and BCA data)
Day 10: Wednesday August 1, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
  • 9:00 – 11:00: Students will prepare pathway analysis presentations
  • 11:00 - 12:00 Webinar: Thermo Scientific on new 13C Compound Discoverer software - TBA

Afternoon
  • 12:00 – 1:00: Lunch - Room 570 -Lee T. Todd Jr. Building Lunch is provided
  • 1:15 – 3:45: Overview of targeted and untargeted direct infusion FTMS:
    • example of polar analyses focusing on amino acids and nucleotides
      • led by Dr. Richard Higashi
  • 4:00 – 6:00: Pathway Tracing using isotopomer and isotopologue distribution data – Part A
    • Led by Drs.Teresa Fan and Andrew Lane,
      • Room 570 Lee T. Todd Jr. Building
Day 11: Thursday August 2, 2018

Morning
  • 8:00 – 9:00: Meet in Room 570 Lee T. Todd Jr. Building Continental breakfast will be provided
    • General introduction to statistics
      • Led by Dr. Hunter Moseley
  • 9:00 – 10:00: Advanced topics/using multi labeled tracers - Led by Dr. Andrew Lance
    • Led by Dr. Hunter Moseley
  • 10:00 – 12:00: Participant presentations and roundtable discussion of pathway tracing assignments

Afternoon
  • 12:00 – 1:00: Lunch - Room 570 Lee T. Todd Jr. Building
    • Lunch is provided
  • 1:00 – 4:00: Pathway Tracing using isotopomer and isotopologue distribution data: Part B*
    • Led by Drs. Teresa Fan and Andrew Lane,
      • Room 570 Lee T. Todd Jr. Building
  • 4:00 – 5:00: Discussion of participants proposed experimental designs
  • 5:00 – 6:00: Ice Cream Social – Room 570 Lee T. Todd Jr. Building
Day 12: Friday August 3, 2018

Morning
  • 8:00 – 8:30 Meet in Room 570 Lee T. Todd Jr. Building
    • Continental breakfast will be provided
  • 8:30 – 11:00 Recap and workshop evaluations
  • 11:00 – 1:00 Lunch/certificates/dismissal

Application Information

Application deadline for the Workshop is July 16, 2018.
  • The 12-day Workshop registration fee is $3,750.
    • This fee includes 12-day workshop, on-campus lodging, and breakfast and lunch each day.
  • Attendees are responsible for their own travel arrangements and costs.
    • Attendees will be accommodated for the extent of the Workshop on campus.
  • Link for location, and building and room specifics: Haggin Hall
  • Some scholarships are available to offset travel costs and registration cost, for students, post-doctoral scholars and fellows whose poster abstracts demonstrate excellence in the science of SIRM.
  • Registration for the 2018 RCSIRM Workshop and Symposium is NOW OPEN: registration link

Symposium - Stable Isotope-Resolved Metabolomics: from bench to bedside

The one-day Symposium on Monday, July 30th, 2018 will feature presentations and poster sessions from leaders using stable isotope-resolved metabolomics (SIRM) as well as other researchers form around the world in a wide range of research.
This is your chance to hear and meet speakers who use stable isotope labeling and other techniques to investigate metabolic changes in many physiological systems and advancing diagnosis and treatment of many clinical conditions, such as GI, and metabolic disorders, and cancer.
  • The Symposium is open to the public.
  • Registration for the Symposium will open at 8:00 am in the Lobby/Atrium newly named the Lee Todd Jr. Building (formerly the Bio Pharmacy Complex).
    • Registration is Free and a continental breakfast, boxed lunch and dinner buffet will be provided free of charge.
  • There will be poster sessions and Sponsor participation.
    • Poster abstract deadline for the Symposium is July 23, 2018.
  • Registration for the 2018 RCSIRM Symposium is NOW OPEN: registration link

Speakers for the 2018 Symposium

The list below are the confirmed speakers for our 2018 Symposium.
  • Gabriela Andrejeva, PhD, Vanderbilt University, TN - presentation
  • Charles Burant, MD, PhD, University of Michigan, MI
  • Marta Cascante, PhD, University of Barcelona, Spain - presentation
  • Teresa W-M. Fan, PhD, Markey Cancer Center, University of Kentucky, KY
  • Gerhard C. Hildebrandt, MD, Markey Cancer Center, University of Kentucky, KY
  • Richard Kibbey, MD, PhD, Yale University, CT - presentation
  • Aalim Weljie, PhD, Perelman School of Medicine, University of Pennsylvania, PA - presentation
  • Susanne Wells, PhD, Cincinnati Children's Hospital, OH - presentation
  • Min Wu, PhD, Beth Israel Deaconess Medical Center, MA
  • Mariia Yuneva, PhD, The Francis Crick Institute, London, United Kingdom

Abstract Submission Guidelines

Abstracts for poster presentations for UK Metabolomics Symposium & Workshop 2018 must be:
  • Submitted by 11:00 pm (EDT) on July 23, 2018, via Word document to Alicia Colliver at ajduna0@email.uky.edu.
  • See Format instructions below.

The Program Committee will review abstracts based on their relationship to human metabolism, novelty, significance of findings and clarity.
  • For questions regarding abstract submission please contact Alicia Colliver at ajduna0@email.uky.edu, or (859) 218-1032

Format

The total character count (including the title and list of authors) may not exceed 4000 characters, including spaces; or 1 page, including any graphical content or Tables.
Each abstract should be sectionalized as follows:
  • Title and Affiliation- first 6 lines.
    • Line 1: Title - maximum 25 words 14 point Bold Arial or Times New Roman. The title should sufficiently represent the content of the abstract. All keywords necessary to identify the subject matter should be included in the title to facilitate electronic retrieval where applicable. Non-standard abbreviations in the title should be avoided. Remainder 11 point Arial or Times.
    • Line 2: Authors - use superscript numbers to refer to affiliations
    • Line 3: Affiliations
    • Line 4: blank
    • Line 5: Abbreviations used in the body of an abstract should be defined at first use.
      • Complex investigational regimens should be clearly identified.
    • Line 6: blank
  • Background - a brief statement indication the purpose(s) of the study
  • Experimental - a brief description of pertinent experimental procedures used.
  • Results - a clear representation of experimental results.
  • Conclusion a statement of conclusion.
  • Acknowledgements - e.g. funding
  • Bibliography

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Topic revision: r23 - 18 Aug 2018, HunterMoseley
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