Enhancing Rigor and Reproducibility in Translational Research Involving Mice
- Graduate Student /Postdoc Registration via https://my.jh.edu/myJH/ EDUCATION SIS/SEAM.
- SOM post-doc fellows submit registration requests via SEAM, using the case reason ‘Add/Drop’ or ‘Interdivisional Registration’, depending on the course. SOM Change of Schedule form, is optional for post-docs and no program director signature is required.
- Section 0002 is a 1 credit, audit option for lectures only (no lab sessions).
- FACULTY/STAFF: should be able to register for audit lecture option via myJH / SIS / SEAM, then request tuition remission via HR.
Since 2010 this has been offered in a short course format, largely for continuity of the practical laboratory training experience.
- Faculty from JHU School of Medicine and Bloomberg School of Public Health introduce concepts in mouse biology, pathology, genetics, normal ‘phenotypes’, concepts and established phenotyping capabilities in multiple disciplines.
- JHU cores and resources are highlighted. See previous course programs/schedules below.
- Syllabus material is provided.
Course Co-Directors: Cory Brayton, DVM, DipACLAM, DipACVP, Jason Villano, DVM, MS, DipACLAM; Jonathan Harrold, ACUC
Course Administrator: Momina Malik mmalik21@jh.edu
This course offers up to ~34 contact hours: ~11hr Laboratory sessions and ~23hr Lectures.
- The three hands-on laboratory sessions include clinical and physical examination of mice, specimen collection, clinical and anatomic pathology.
- Familiarity with basic anatomy and with the laboratory manual is expected for participation in laboratory sessions.
- JH Graduate students taking this course FOR CREDIT must participate in laboratory sessions
- Laboratory Manual, Lecture material and resources are provided electronically, it is NOT necessary to purchase a text book.
Learning Objectives (goals): Students completing this course will be able to:
- Critically analyze and select mouse models and conditions for research aims;
- Select and Implement humane and useful procedures for research aims;
- Plan for analyses, pathology, histology, to achieve useful specimens and data.
OVERALL AIM (Learning Outcome): Achieve Rigor, Reproducibility, Validity, Translatability in research involving mice, using practical skills, and resources, from the course, for the humane and optimal use of mice and GEM in translational research.
Credit/grade based on:
- Lab participation (required).
- IN person lecture attendance is expected unless excused. Daily AM /PM sign in.
- Quiz A brief (Qualtrics) survey relevant to articles for the group project.
- Quiz B (in Canvas) write/draft Animal portions of your Methods sections for a paper, an example/template is provided.
- Group Project: 3 or 4 groups will each assess ‘methods’ of an influential article; (everyone will read excerpts to complete quiz A). On Friday morning each group will present the strengths and weaknesses of their article, and its methods reporting, in 10 or fewer minutes, and 10 or fewer PPT (or similar) slides, and the class will discuss ~10min per article. PPT template is provided – alternative presentation options are welcomed.
Phenotyping Program Schedule
Current information/program is updated in CANVAS
MONDAY ~ 9am-5pm
THEME: Phenotyping & Research Relevant Mousology
Registration Starting ~8:30am
- Introduction: Phenotyping, Mouse pathobiology & Famous Mice
- Common Phenotypes & Disease (Spontaneous/NON infectious & research impacts)
- External Environmental (X) Factors (& research impacts)
- INFO On Quizzes & Group PROJECT
LUNCH break – Meet Participants/Cores/Group Work
- Microbial & infectious Research Challenges (& research impacts)
- Immunovariability (immune sufficient and immune deficient) mice (& research impacts)
- Research relevant social life and behaviors of mice (& research impacts)
TUESDAY ~ 9am-5pm
THEME: GEM & Multidisciplinary Phenotyping
- Making Mice – traditional and new transgenic technologies
- Metabolic Phenotypes and Phenotyping
- Pulmonary/Respiratory Phenotypes & Phenotyping
LUNCH break – Meet Participants/Cores/Group Work
- IMAGING for Phenotyping MALDI optical PET CT MRI etc
- Ophthalmic Phenotypes and Phenotyping
- Auditory Phenotypes and Phenotyping
WEDNESDAY ~ 9am-5pm
THEME: Practical Phenotyping 1
JH Phenotyping Laboratory Manual
Participants should REVIEW by Wednesday AM
- Clinical/Physical Exam CSD, Modified SHIRPA
- Practical Clinical Pathology (Hematology Chemistry etc for research)
LUNCH break – Meet Participants/Cores/Group Work
- LAB 1, 2: Clinical/Physical Exam; Common procedures and Specimen collections
- Discussion of participants questions/interactive REVIEW (Quiz format)
THURSDAY ~ 9am-5pm
THEME: Practical Phenotyping 2: Pathology
- Practical Pathology – Necropsy, examination, tissue collection trimming
- Comparative Anatomy/Pathology (human/mouse)
LUNCH break – Meet Participants/Cores/Group Work
- LAB 2: Anatomic Pathology – Necropsy, examination, tissue collection
- Discussion of participants questions/interactive REVIEW (Quiz format)
FRIDAY ~ 9am-4pm
THEME: Practical Pathology + Special Techniques
- LAB 3: Tissue Trimming for histopathology (& project aims)
GROUP PROJECT PRESENTATIONS + Quiz A (Review)
LUNCH break – Meet Participants/Cores (+/- preclinical study cases)
- Practical Pre GLP Pathology (efficacy/safety assessments in academic settings)
- Immunohistochemistry Principles and Practice
- Digital Pathology: image analysis and quantitative pathology
- Embryo and Developmental Phenotyping
- Pathology Faculty Discussion of participants research questions
5pm – Quiz B Due! (= Methods Section for your next Paper)
PARTICIPATING CORES
PhenoCore Phenotyping and Experimental Pathology Core (MRB)
iLAB information and submission https://johnshopkins.ilab.agilent.com/landing/42/
Animal Care and Use Committee (ACUC)
Applied Imaging Mass Spectrometry (AIMS) Core
iLAB information and scheduling https://johnshopkins.ilab.agilent.com/landing/42/
Behavioral Core SOM (MRB)
iLAB information and scheduling https://johnshopkins.ilab.agilent.com/landing/42/
CSMR Centralized Services for Metabolism Research
Indirect calorimetry, food intake, QNMR, etc
iLAB information and scheduling https://johnshopkins.ilab.agilent.com/landing/42/
ES Cell and Transgenic Core
Johns Hopkins Transgenic and ES Cell core https://www.hopkinsmedicine.org/core/Home.htm
MRB Molecular Imaging Core
MRI, PET, CT, SPECT, IVIS, Optical Imaging, Ultrasound (MRB) https://www.hopkinsmedicine.org/radiology/research/service-cores/mrb-service-center-lab/index.
OTS Oncology Tissue Services Core
TMA, IHC, Slide Scanning, Histology core labs at SKCCC
iLAB information and submission https://johnshopkins.ilab.agilent.com/landing/42/
Laboratory Manual and Previous Programs
Phenotyping Laboratory Manual 6th ed rev 2025
2025 Schedule of Lecture and Laboratory Topics and Faculty
2024 Schedule of Lecture and Laboratory Topics and Faculty
2023 Schedule of Lecture and Laboratory Topics and Faculty
2021 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2020 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2019 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2016 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2015 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2013 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2012 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2011 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2010 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2008 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2007 Schedule of Lecture and Laboratory Topics and Faculty (PDF)
2009 Phenotyping Symposium (PDF)
2008 Phenotyping Symposium (PDF)
2007 Phenotyping Symposium (PDF)
2006 Phenotyping Symposium (PDF)
ADDITIONAL MATERIALS RESOURCES
- Research-Relevant Conditions and Pathology of Laboratory Mice, Rats, Gerbils, Guinea Pigs, Hamsters, Naked Mole Rats, and Rabbits.
Cooper TK, Meyerholz DK, Delane Piersigilli A, Southard TL, Brayton CF. ILAR J. 2022. - Research-Relevant Clinical Pathology Resources: Emphasis on Mice, Rats, Rabbits, Dogs, Minipigs, and Non-Human Primates.
Bau-Gaudreault L, Arndt T, Pro Brayton. ILAR J. 2021. - Research Relevant Background Lesions and Conditions: Ferrets, Dogs, Swine, Sheep, and Goats.
Helke KL, Meyerholz DK, Beck AP, Burrough ER, Derscheid RJ, L EF, Scu CL, Brayton CF. ILAR J. 2021. - Research-Relevant Background Lesions and Conditions in Common Avian and Aquatic Species.
Mangus LM, França MS, Shivaprasad HL, Wolf JC. ILAR J. - Research Relevant Conditions and Pathology in Nonhuman Primates.
Saravanan C, Flandre T, Hodo CL, Lewis AD, Mecklenburg L, Romeike A, Turner OC, Yen H. - Immune Relevant and Immune Deficient Mice: Options and Opportunities in Translational Research.
Radaelli E, Santagostino SF, Sellers RS, Brayton CF. ILAR J.
