Seth Newsome (SDN)

[email protected]

Emma Elliott Smith (EES)

[email protected]

Lab Coordinator

Alana Robinson (AR)

[email protected]

BIOL 419/519

PAIS 2120
Lecture: Tuesday & Thursday 9:30–10:45AM
Lab: Wednesday 2:00–4:00PM

Course Syllabus
Reading Report Form
CSI Sample Submission Form

Course Schedule

Week 1

August 22nd: Introductions, Expectations, and Isotopic Definitions

Lab (8/23): Group Project Discussion and Form Groups

August 24th: Definitions and Fractionation* (EES)

Reading: *Ben-David and Flaherty 2012.pdf; Newsome et al. 2007.pdf

Week 2

August 29th: Isotopes in Water (SDN)

Lab (8/30): Research Questions and Experimental Design

August 31st: Isotopes in Plant Water* (SDN)

Reading: *Dawson 1998; Bowen et al. 2005.pdf

Assignment Due (9/1): Ideas for Group Projects (10 Points)

Week 3

September 5th: Primary Producer Carbon I (EES)

Lab (9/6): Introduction to Gear I: CSI Tour (EA/TCEA/GB–IRMS)

September 7th: Primary Producer Carbon II* (EES)

Reading: *Driscoll et al. 2020.pdf; Cerling et al. 1997.pdf

Week 4

September 12th: Primary Producer Nitrogen (SDN)

Lab (9/13): Sample Preparation I: Decalcification, Lipid-Extraction, Microbalance; Sample Preparation Protocols

September 14th: Primary Producer Nitrogen* (SDN)

Reading: *Austin and Vitousek 1998.pdf; Amundson et al. 2003.pdf

Assignment Due (9/15): Project Description and References Guidelines (40 points)

Week 5

September 19th: Consumer Carbon (EES)

Lab (9/20): Sample Preparation II: Sample Homogenization, Cryodistillation

September 21st: NO CLASS (High School IsoCamp)

Reading: Kelly 2000.pdf

Week 6

September 26th: Consumer Carbon* (EES)

Lab (9/27): Introduction to Gear II: CSI Tour (GCC–IRMS and Picarro)

September 28th: Consumer Nitrogen (SDN)

Reading: *Kurle et al. 2014.pdf; Vanderklift and Ponsard 2003.pdf

Week 7

October 3rd: Consumer Nitrogen* (SDN)

Lab (10/4): Mixing Models (SDN); Linear Mixing Model Exercise; Phillips and Koch 2002.pdf

October 5th: Isotopic Incorporation (SDN)

Reading: *Croll et al. 2005.pdf, Moore et al. 2016.pdf

Week 8

October 10th: Consumer Hydrogen* (SDN)

Lab (10/11): FALL BREAK (NO CLASS)

October 12th: FALL BREAK (NO CLASS)

Reading: *Estep and Dabrowski 1980.pdf; Hobson et al. 1999.pdf

Assignment Due (10/11): Experimental Design and Methods Guidelines (50 Points); Example: SEV Smammals

Week 9

October 17th: Consumer Sulfur (SDN)

Lab (10/18): Data Reduction: IsoCamp 2022 Plants RAW; CSI Working Standard Values

October 19th: Consumer Oxygen (EES)

Assignment Due (10/20): Linear Mixing Models

Week 10

October 24th: Amino Acid Carbon (EES)

Lab (10/25): Bayesian Mixing Models (SIMMR); R Installation Instructions; SIMMR Assignment; SIMMR Assignment Data

October 26th: Amino Acid Carbon* (EES)

Reading: *Elliott Smith et al. 2021.pdf; Larsen et al. 2009.pdf; O'Brien et al. 2002.pdf; Phillips et al. 2014.pdf

CLASS SIMMR DEMO: SIMMR Code; geese; sources; corrections; SIMMR GitHub

Week 11

October 31st: Producer Amino Acid Nitrogen (SDN)

Lab (11/1): Group Work Time

November 2nd: Consumer Amino Acid Nitrogen* (SDN)

Reading: *McMahon and McCarthy 2016.pdf; Ramirez et al. 2021.pdf

Assignment Due: Bayesian Mixing Model Exercise (November 3rd)

Week 12

November 7th: GUEST LECTURE (Mertz)

Lab (11/8): Spatial Metrics (SIBER); SIBER Assignment; SIBER Assignment Data

November 9th: GUEST LECTURE (Busquets-Vass)

Reading: Newsome et al. 2020.pdf (11/7); Busquets-Vass et al. In Review.pdf (11/9)

CLASS SIBER DEMO: SIBER Code; Demo Sea Otter Data

Week 13

November 14th: Amino Acid Hydrogen* (SDN)

Lab (11/15): Group Work Time: Draft Figures

November 16th: Fatty Acid Carbon and Hydrogen (SDN)

Reading: *Fogel et al. 2016.pdf; Wang et al. 2015.pdf; Ruess and Chamberlain 2010.pdf

Assignment Due: SIBER Exercise (November 17th)

Week 14

November 21st: Data Statistical Session: Essential AA LDA Demo; LDA Assignment; Producer_Library



Project Pre-Proposal Guidelines; Oral Presentation Evaluation

Week 15

November 28th: Data Statistical Session: Essential AA LDA Demo; LDA Assignment; Producer_Library

Lab (11/29): Group Work Time

November 30th: GUEST LECTURE (Neff)

Assignment Due: Submit Project Pre-Proposal for Peer Evaluation (Wednesday November 29th); Peer Review Guidelines

Week 16

December 5th: Group Project Presentations

Lab (12/6): Group Project Presentations

December 7th: Group Project Presentations

Assignment Due (12/6): Project Pre-Proposal Peer Evaluations

Final Pre-Proposal Due: Monday December 11th

Supplemental Readings