Nanocourses in Biomedical Sciences

Graduate Course Selection Book

Nanocourses are short courses that meet for a total of ~7-8 hours and typically address a new or evolving area that is not covered by the standard graduate curriculum. The course could be given in a week or two days or even over 7 weeks.

Each Nanocourse is worth 0.5 credits.
Grading is Satisfactory/Unsatisfactory

To request course, please submit the Nanocourse Request form to Cheryl Small in the College of Graduate Studies, Room 3122 WH.
At least 3 students' names must be on the request form for the course to be offered.
Following submission of the form, faculty will work with students to arrange timing of the course.

Nanocourses

GS647-001 Nanocourse: Emerging Infectious Diseases
Course Instructor(s): Mark Polhemus, MD, with instruction assistance of Kristopher Paolino, MD, Christina Lupone, MPH, Aaron Glass, PhD, Lisa Ware, James Vossler, MS, Timothy Endy, MD, MPH
Enrollment limit: 10
Brief Description:

  1. Background Factors Impacting Emerging Infectious Diseases- Drivers of Disease Emergence from Ecology to Epidemiology
  2. Factors of Emergence in Anti-Microbial Resistance: A Look into the Threat of Tuberculosis, Malaria, Gram Negative Bacteria, and Gonorrhea
  3. Arboviruses and Hemorrhagic Fever Viruses- You Pick One and We Discuss
  4. Influenza: Pandemic Immunology
  5. Immunology of HIV/AIDS and Emerging Issues in STD’s
  6. Current Laboratory Capacity for EID’s: A Perspective from a Hospital Microbiologist
  7. Global Preparedness and Field Responses - Microbiology and Immunology Tools for the Scientist

GS647-002 Nanocourse: Introduction to Flow Cytometry
Course Instructor(s): Steven Taffet, PhD, Aaron Glass, PhD, Lisa Phelps
Enrollment limit: 6 
Brief Description: Classes will include: Introduction to flow, Design of antibody panels, Hands on training on the cytometer, Analysis of Flow Data (FloJo), New trends in flow cytometry

GS647-003 Nanocourse: Mitochondrial DNA Replication- Un muddling the field
Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: 10
Brief Description: 4, 2 hour classes over a 4 week period. Cover recent papers in yeast and mammalian cells that disagree on the mode of DNA replication in mitochondria. The class will require students to read several papers each week and be ready to discuss them.

GS647-004 Nanocourse: Radiobiology
Course Instructor(s): Jason Horton, PhD, Sandra Hudson, PhD and Paul Aridgides MD
Enrollment limit: 20
Brief Description: Ionizing radiation is used as a cytotoxic agent in biomedical applications. This course will review the unique aspects of ionizing radiation as physical entity, and its atomic, molecular and physiological effects on living cells and tissues. Topics to be discussed will include radiation effects on cellular biology, oxidative stress and free radical chemistry, applications in cancer therapy, experimental model systems, adverse events and toxicity associated with radiation exposure, and clinical translation of basic radiobiology to the practice of radiation oncology. The course will be presentation/discussion based, and supplemented by readings assigned by the instructors. Student performance will be assessed on the basis of participation in in-class discussion and completion of two home-work assignments.

GS647-005 Nanocourse: Vaccine Development
Course Instructor(s): Mark Polhemus, MD, with instruction assistance of Kristopher Paolino, MD, Christina Lupone, MPH, Aaron Glass, PhD, Lisa Ware
Enrollment limit: 10
Brief Description: Vaccine Development nanocourse will feature 7 one-hour lecture and discussion sessions of the following:

  1. Introduction: The Historical Impact of Vaccines on Disease Epidemiology and the Economic Burden of Vaccine Development
  2. The History of Regulatory Affairs and Oversight of Vaccine Development
  3. Vaccines and Immunological Memory
  4. Vaccines as Therapeutics: How to fight Cancer with Vaccines
  5. Advances in Vaccine and Immunization Technologies
  6. Debate Arguments on Vaccine Safety: Anti-Vaxxer versus Pro-Vaxxer
  7. New Vaccines: Challenges and Prospects in Development

GS647-006 Nanocourse: What Do I do next?
Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: 8
Brief Description: The class will have 4, 2 hour sessions over a four week period. Each week 1-3 papers will be assigned. In class student will discuss the papers and will work on where the research is going, how one would decide the best course of action to progress the field further. Topics will delve down into what experiments should be done next, how those experiments should be set up, expected results, etc.

GS647-007 Nanocourse: Measuring binding affinities of biomolecules using multiple techniques
Course Instructor(s): Stewart Loh, PhD and Thomas Duncan, PhD
Enrollment limit: 10
Brief Description: This is primarily a laboratory course in which students will receive hands-on training on how to detect and quantify interactions between biomolecules (proteins, nucleic acids) and their binding partners (proteins, peptides, nucleotides, small molecules, and drugs). Students will be tasked with measuring binding affinities of several examples of the above interactions. Students will design binding experiments to be carried out using three types of instruments: (1) fluorescence plate reader, (2) isothermal titration calorimeter, and (3) biolayer interferometer. Students will prepare samples, perform the experiments on each of the three instruments, and analyze the binding data using the manufacturer’s software. This course is meant to provide students with theoretical knowledge as well as practical experience that will help them in their own research projects.

GS647-008 Nanocourse: Bone Biomechanics
Course Instructor(s): Kenneth Mann, PhD
Enrollment limit: 8
Brief Description: This course will cover mechanical aspects of skeletal bone using material and structural frameworks. Basic solid mechanics concepts such as stress, strain, deformation, elasticity, plasticity, and visco-elasticity will be explored. Structural mechanics concepts will include simple beam theory and how this can be used with CT image sets and the BoneJ plugin via IMAGEJ. Experimental approaches to determine bone material/structural properties will be introduced to determine bone properties from larger (human) and small laboratory animal tissue. One hour interactive lecture format over seven weeks. At the end of the course, the student will have basic background needed to perform, interpret, and analyze biomechanics experiments on small bone specimens commonly used in orthopaedic research. The course will require student to complete short problem sets to reinforce main concepts. Assessment of student performance will be based on participation during in-class discussion and completion of home-work assignments.

GS647-009 Nanocourse: SURF Journal Club
Course Instructor(s): Michael Cosgrove, PhD
Enrollment limit: 6 (or 12)
Brief Description: The main goal of this nanocourse is to give graduate students the opportunity to obtain teaching experience by running a journal club for Summer Undergraduate Research Fellowship (SURF) students. Students will have the opportunity to organize, moderate, and evaluate journal club participation by a small group of 5-6 Fellows. Graduate students will meet with Fellows once a week starting the second week of June and running until all Fellows have presented. Graduate students will also meet with the course instructor at the beginning and end of the journal club program for mentoring, advice, and feedback.

GS647-010 Nanocourse: Manuscript Submission
Course Instructor(s): Julio Licinio, MD,PhD
Brief Description: How to prepare, submit and resubmit...

GS647-011 Nanocourse: Introduction to Single-Molecule Fluorescence Microscopy
Course Instructor(s): Dr. Michael Börsch, Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena
Enrollment limit:10
Brief Description: In conventional microscopy experiments fluorescence data are acquired from a large number of molecules. Since many molecules are interrogated simultaneously, their properties are averaged out. In contrast single-molecule experiments provide a wealth of information like time trajectories of conformational dynamics of enzymes. The course gives an introduction to single-molecule imaging and spectroscopy and analysis tools of the data.
Topics Covered:
  1. Introduction - 25 years of single molecule detection
  2. Photophysics and Photochemistry of single molecules
  3. Single-molecule anisotropy and Förster resonance energy transfer (smFRET) measurement

GS647-012 Nanocourse: Protein Expression & Purification
Course Instructor(s): Alaji Bah, PhD
Enrollment limit: 10
Brief Description: In this nanocourse, we will focus on strategies to recominantly express and purify folded and intrinsically disordered proteins using E. coli and standard chromatographic techniques respectively. We will first discuss how to obtain the cDNA of your gene of interest, the variety of expression vectors available, cloning straties, E. coli strains available, pilot expression schemes, scaling up to meet your needs etc. Then, then we discuss how we can use the physico-chemical properties and the biological function(s) of the protein to guide our purification strategies. We will discuss the concept of protein ‘purity’ (how pure should your protein be?). Finally, we’ll explore how we can ‘verify’ that our purified protein is your protein of interest and that it’s ‘functional’. All these discussions will be accompanied by demonstration of the expression/purification of a protein from my lab.

GS647-013 Nanocourse: Bioinformatics I: Introduction to Bioinformatics
Course Instructor(s): Vladimir Kuznetsov, PhD
Enrollment limit: 3-15
Brief Description: Bioinformatics: The big picture. Definitions and branches. Links to other disciplines: Biotechnologies, Genomics and Systems biology, Big Data Science, Computing, Statistics, Evolution, Integrative and Predictive Medicine. Nomenclature and annotation systems. Gene ontology. Genome, transcriptome and proteome complexity. Bioinformatics database, web tools and software. Major data bases, web sites and software for analyze of DNA, RNA, and protein sequences.  Microarrays, the next generation sequences and basic bioinformatics tools for big data analysis. Sequences obtaining and comparison. Paired and multiple alignments software. Data formats.  Blast, BLAT, other similar software. Integrative bioinformatics strategies. Basic probability theory and statistical methods in bioinformatics. Enrichment and correlation analyses. Network and pathways analysis tools. Comparative evolution. Aligned sequences as phylogenetic trees.

GS647-014 Nanocourse: Bioinformatics II: Integrative Strategies in Biotechnology and Medicine
Course Instructor(s): Vladimir Kuznetsov, PhD
Enrollment limit: 3-15
Prerequisite: GS647-013
Brief Description: Human genome, The Encyclopedia of DNA Elements(ENCODE), TCGA and other omics projects. Mapping and data integration. Basic functional genomics and transcriptomics tools. Non-coding DNA and RNA. RNA-seq, Chip-Seq, CHIA-PET, CAGE, DRIP-seq methods. Transcription factors and position-specific matrixes. Transcription regulation. Genome and transcriptome structures and complex architectures.  Network analysis and pathways.  Non-canonical structures and their analysis. RNA-DNA-protein interactome. Disease critical genome regions identification.  TCGA Genome portal and tools. Computational biology, bioinformatics, integrative genomics and predictive oncology. Cancer classification, patient’s prognosis, disease prediction and novel biomarker discovery.

GS647-015 Nanocourse: Computer ABC for Biologists
Course Instructor(s): Chunyu Liu, PhD and Chunling Zhang, MS
Enrollment limit: 10
Prerequisite: Students should bring their own laptops (PC or Mac) with VPN access to the University networks, and will need to install a few software (to be specified) after registering the class.
Brief Description:  We will introduce basic about computer to biologists, who are interested in either becoming professional bioinformaticians, data analysts, or using bioinformatics tools to analyze their own experimental data. In the 7-hour course, we will describe basic concepts of hardware and software, parts of computers, networks and supercomputers, major OS, file systems and directory, file types and contents, network protocols. We will provide students the first hands-on experience on real working environment of professional bioinformaticians. We guide students to plan for their future in the bioinformatics world.

GS647-016 Nanocourse: New Developments in G-protein Coupled Receptor (GPCR) Research
Course Instructor(s): Barry Knox, PhD
Enrollment limit: None
Brief Description: The purpose of this course is to familiarize the student with new developments in the accelerating world of G-protein coupled receptor research. The course will be a combination of lecture presentation and discussion of recent advances. Students are encouraged to bring their interest in a particular receptor or biological process for discussions. The following topics will be covered in separate sessions:

  1. Introduction to GPCRs and their Evolutionary History (1 hour)
  2. New GPCR Methodology: Signaling, Structure and Screening (2 hours)
  3. GPCR in silico (1 hour)
  4. GPCRs: Invertebrates and Orphans (2 hours)
  5. Psychedelic GPCRs (1.5 hours)
  6. Adhesion GPCRs (1.5 hours)

Required reading (2 articles/session) will be assigned for discussion to follow a presentation led by instructor. Additional topics can be included upon request.

GS647-017 Nanocourse: Neuroinflammation of the Human Brain and Mind 
Course Instructor(s): Cyndi Shannon Weickert, PhD
Enrollment limit: 12
Brief Description: This course will begin by reviewing the evidence that mental illness (depression and schizophrenia in particular) can be understood as disorders of the immune system. Next, we will cover the evolving terminology used in the field of neuroinflammation from the perspective of the body and the brain. Then, we will discuss examples from known neurodegenerative disorders to better understand how neuronal signals stimulate a glial inflammatory reaction. We will contrast the neurotrophic and neurotoxic roles of astrocytes and microglia in brain inflammation. Lastly, we will consider the role of peripheral immune cells in aggravating or possibly ameliorating brain tissue damage. The course will involve reading outside the classroom, lecture presentations, discussion of several recent journal articles and written assessments.

The following topics will be covered in separate sessions:

  1. Introduction to Innate and Adaptive, Acute, Chronic and “Sterile” Inflammation in Brain (1.5 hour)
  2. Lessons learned from classically defined neuroinflammatory conditions (1.5 hours)
  3. The double-edge sword of brain glia (1.5 hour)
  4. Our changing understanding of microglial and microglial-like cells (1.5 hours)
  5. Just who is getting across the “Berlin Wall” of the brain? And how? (1.5 hours)
  6. What can Immunologist teach Psychiatrists and vice versa? (1.5 hours)

Required reading: Students will be expected to read the book “The Inflamed Mind” by Edward Bullmore prior to class. At least four chapters from the text book “Neuron-Glia Interaction in Neuroinflammation” Edited by Akio Suzumura and Kazuhiro Ikenaka, will be assigned reading prior to a presentation and discussion led by instructor with 1-2 students assigned as co-discussants. Journal articles (n=4) will be assigned reading to supplement the text book. Students are expected to complete the reading and be prepared for in class discussions. To test if basic concepts of neuroinflammation have been learned and can be applied, students are expected to answer 4/6 short essay questions in less than half a page. The set of questions will be given during the first day of class and will be expected to be completed and turned in on the last day of class.

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