Alliance for Global Health and Science 2019 Summer Institute
About the Alliance Summer Institutes: Through our annual summer institutes at Makerere University, we have trained over 200 undergraduate and graduate students from the College of Health Sciences since our first institute in 2016. Student participants consistently provide positive feedback of their experience with the institute, and the impact goes beyond just words – we have seen improved production capacity and research outputs as a result of the trainings. From these investments and interactions the Alliance is a growing web of scientific collaborations, both North/South and South/South training exchanges and a needs-based awareness that are empowering local scientists to drive basic research and develop novel solutions geared toward the prevalent diseases in the region.
The Alliance has held three summer Institutes to strengthen scientific capacity among students and staff researchers. The two-week Institute includes concurrent intensive short-term workshops taught by US faculty and their graduate students and ranging from 5-10 days each. These workshops focus on both laboratory skills and “soft” or theoretical skills. The second component of the Institute is a series of seminars by US and Ugandan faculty. Participants are drawn from the Makerere College of Biomedical Sciences, School of Public Health and School of Medicine.
The Summer 2019 Institute
July 29 – August 10th
Workshops:
- High Throughput Sequence Bacterial DNA Variant Analysis
- Application of Epidemiological Thinking and Methods to Infectious Diseases
- Introduction to Scientific Grantwriting and Presentation
- Introduction to Molecular Cloning
- Purification of CRISPR?Cas9 for pathogen detection in complex human samples
- Basic concepts and techniques in innate immunity
Workshop Descriptions:
High Throughput Sequence Bacterial DNA Variant Analysis
Instructors: Dr. Matthew Settles, Sserwada Ivan, Gerald Mboowa, Savannah Mwesigwa
This workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools associated with command-line DNA variant analysis. Participants will explore experimental design, cost estimation, data generation, and analysis of DNA sequence data generated on the Illumina sequencing platform. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed with provided datasets, using command-line interaction and R.
Application of Epidemiological Thinking and Methods to Infectious Diseases
Instructor: Dr. Art Reingold
Infectious diseases continue to cause substantial morbidity and mortality globally, especially in resource poor countries, despite the availability of many vaccines and other prevention strategies. This workshop will focus on how epidemiologists conceptualize and design both experimental and observational studies intended to improve our understanding of the risk factors for and the efficacy/effectiveness/impact of diverse prevention and control strategies. The infectious diseases and examples discussed will primarily come from Sub-Saharan Africa.
Introduction to Scientific Grantwriting and Presentation
Instructors: Dr. Nevan Krogan, Jacqueline Fabius
This workshop is geared towards providing assistance to prospective grant applicants in developing a competitive scientific grant application step-by-step, as well as guiding participants in the fundamentals of presenting scientific research to both scientific and non-scientific audiences.
Introduction to Molecular Cloning
Instructors: Dr. Jeff Cox, Daniel Licht, Eli Dugan
Students will learn the history of molecular cloning – the synthesis of recombinant DNA – including classical restriction enzyme cloning, as well as the latest technological advancements in field such as Golden Gate cloning, Gibson cloning, and SLiCE cloning. Students will learn how to use software to design and synthesize DNA constructs containing their gene of interest into an expression vector. We will then perform the standard protocols for molecular cloningPCR amplification of DNA of interest, gel electrophoresis, gel extraction/ DNA purification, DNA assembly, bacterial transformation, and sequence validation of the newly synthesized plasmid. Students will learn about the properties and uses of fluorescent proteins in molecular and cell biology as we use GFP and RFP as examples of genes that can be cloned into vectors and used as tags. We will then finish the workshop focusing on an advanced technique known as CRISPRi, to demonstrate how molecular cloning techniques learned in the course can be used to repress the expression of a gene of interest.
Protein Purification of CRISP/Cas9 for pathogen detection in complex human samples
Instructors: Dr. Oren Rosenberg, Vida Ahyong, Amy Diallo
The workshop will focus on the expression and purification of Cas9-mCherry. The methodology of protein engineering will be discussed, including the design of an active Cas9 complex (Cas9 protein complexed to a small guide RNA). Students will first induce protein expression and employ purification techniques to isolate Cas9. Students will be instructed on how to prepare an SDS-pAGE gel for analysis. With the protein product, we will learn to assay for enzyme activity for a specific target sequence using a small guide RNA. We will discuss next generation sequencing with a focus on understanding what the data is and how we process these large datasets. Then we will discuss metagenomic sequencing for pathogen identification and detection using an online portal called, IDseq. Finally we will apply what we learned to identify pathogens in clinical samples from Uganda.
Basic Concepts and Techniques in Innate Immunity
Instructors: Dr. Sarah Stanley, Derek Bangs, Dr. Matthew Knight
Innate immune cells such as macrophages and dendritic cells are critical both for sensing the presence of invading pathogens and for initiating immune responses that lead to control of infection. IN addition, macrophages serve the dual role as both the main effectors of antimicrobial function and the host cell for most successful bacterial pathogens. This workshop will combine an investigation into concepts of innate immunity with basic technique in tissue culture and laboratory-based analysis of immune responses. Concepts covered will include: how do innate immune cells distinguish pathogens from non-pathogens? How does this influence subsequent cytokine production and activation of adaptive responses? How do innate immune cells control infection with pathogens? In the lab, students will explore differences in activation of macrophages by extracellular and cytosolic receptors using both sterile stimulation and infection with bacterial pathogens. Immune responses will be analyzed using flow cytometry, ELISA, qPCR and other basic immunological techniques. This workshop will incorporate classroom lectures and discussions of the primary literature with wet-lab experience with an emphasis on state-of-the-art concepts in innate immunity, rigorous experimental design, and critical thinking skills.