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Gen 575: Fundamentals of Biomedical Instrumentation

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Gen575

Gen 575: Fundamentals of Biomedical Instrumentation

Course description

An introduction to the fundamentals of instrumentation commonly used in biomedical research settings including mass spectrometers, optical microscopes, and DNA sequencers. Emphasis on a practical understanding of the physical and chemical properties that underlie operation and sources of uncertainty, noise, and error.

Instructional staff

Michael MacCoss, PhD
Brian Beliveau, PhD

Meeting times and locations

Spring Quarter 2024: Mondays & Wednesdays 10:30–11:50 am, Foege S-110

Prerequisites

Background in molecular and cellular biology, chemistry, genetics, biochemistry, engineering, or related discipline and experience with quantitative problem solving.

Course materials

There is no one textbook that can effectively cover the information presented in this course. To supplement the lecture content, the instructors will assign supplemental readings from reviews, historical papers, and/or free online sources.

Course requirements

Late homework will be accepted, but penalized. Specifically, each assignment is worth 100 points, from which 10 points will be deducted for each day (or fraction thereof) that you turn it in late. The maximum deduction for being late is 60 points (even if you are more than 6 days late).

Students may miss lectures without suffering a penalty to their participation grade provided that their absence is cleared with an instructor. While we realize it may not always be possile to do this in advance (eg, becauese of illness or emergency), but we please ask when possible that we be given >1 week notice. 5% will be deducted from the class participation grade for each uncleared absence.

Course grade

Participation: 60%
Problem sets: 40% (4, worth 10% each).

Course format

Each 80-minute class will be divided between lecture content about an instrumentation topic, discussion, and problem solving exercises related to the lecture topic.

Lecture Topic Date Instructor Slides Readings Assignments
1: Intro, Information Currencies 03/25/2024 Brian/Mike 1.Intro.Information.Currencies 1.NASA.EM.book
1.NASA.EM.graphic
1.NIST.SP.1247
2: Information Theory 03/27/2024 Brian 2.Information.Theory 2.Guardian.Fourier.Transforms
2.Guardian.Shannon
2.Sampling
3: Evaluating Information 04/01/2024 Brian 3.Evaluating.Information 3.ejifcc.testing.pdf
3.Montparnasse.Accident.pdf
Problem Set 1
4: Why Tech Dev? 04/03/2024 Mike 4.WhyTechDev 4.ScienceTechnology.Brooks
4.Annurev.Anchem.Hood
5: Signal-to-noise 04/08/2024 Mike 5.SignalNoiseBias 5.Agilent.Signal-Noise
5.JCE.SN.Coor
5.JCE.ShotNoise.Mclain-Wright
6: Quantitative Analysis 101 04/10/2024 Mike 6.Quant101.Calibration 6.NIST.Calibration
6.LOB-LOD-LOQ.Armbruster
6.Shimadzu.TOF.Calibration
7: Basics of Biomedical Separation 04/15/2024 Mike 7.Separations 7.Chrom.FigsMerit.Agilent
7.Laemmli-SDSPAGE
7.OFarrell.2DGel
7.CentrifugationSeparations
8: Mass Spectrometry 1: Ionization and Mass Analyzers 04/17/2024 Mike 8.MS.Ionization.Analyzers 8.ElectrosprayReview
8.Quadrupole.JCE1986
8.IonTraps.March
8.MALDIReview.Hillenkamp_et_al
9: Mass Spectrometry 2: Intro to qualitative peptide and protein analysis 04/22/2024 Mike 9.QualitativePeptideAnalysis 9.ResidueMass.Table
9.HuntSpectraInterpretation
9.KinterAndSherman-Chapter4
10: Mass spectrometry 3: Quantitative Analysis 04/24/2024 Mike 10.QuantitativeProteomics 10.IsobaricMassTags.MCP
10.SWATH.MCP
11: Proteomics: Alternatives to mass spectrometry 04/29/2024 Mike 11.Non-MSBasedProteomics 11.Alfaro.NatMeth.SingleMol
11.Gold.Aptamer.SomoScan
11.MacCoss.NatMeth.SingleMol
12: Spatial and Single-cell Proteomics 05/01/2024 Mike 12.SpatialProteomics
13: Light Sources 05/06/2024 Brian 13.Light.Sources 13.Laser.History
13.Lamps
14: Multispectral imaging 05/08/2024 Brian 14.Multispectral.Imaging 14.Chroma.dichroics
14.Edmund.filters
15: Fluorescent labels 05/13/2024 Brian 15.Fluorescent.Labels 15.Dyes
15.GFP.history
16: Optical detection 05/15/2024 Brian 16.Optical.detection 16.FACS.detectors
16.Prime95B.sCMOS
16.Zeiss.PSF
Problem Set 4
17: Objectives and PSFs 05/20/2023 Brian 17.Objectives.PSFs 17.Olympus.Decon
17.Photometrics.SDC
18: Guest lecture: Light Sheet Microscopy 05/22/2023 Brian Guest Lecture from Adam Glaser 18.Glaser.eLife.2024
Please come prepared with ≥1 question to ask Adam

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