Instructors:
Lead: Professor Michele Nishiguchi, Department of Molecular and Cell Biology
(nish@ucmerced.edu)
Co-Lead: Professor Chris Amemiya, Department of Molecular and Cell Biology
(camemiya@ucmerced.edu)
Prerequisites: High school biology required; AP Biology or chemistry helpful but not
required. All safety training and technical instruction provided. Most important:
enthusiasm for hands-on research and willingness to work collaboratively with live
organisms!
DESCRIPTION
Imagine a newly hatched squid, no bigger than a grain of rice, swimming in the dark
ocean. Within hours, its body begins to glow with soft blue light—not from magic, but
from billions of light-producing bacteria colonizing a special organ in its body. In this
cluster, you’ll explore one of nature’s most fascinating partnerships: the symbiosis
between the Hawaiian bobtail squid and its glowing bacterial partner, Vibrio fischeri.
What You’ll Do: Working in research teams, you’ll culture bioluminescent bacteria and
watch them glow in your hands. You’ll use microscopes to observe how bacterial
infection triggers dramatic changes in squid development. You’ll extract DNA, run PCR
experiments, and explore cutting-edge CRISPR gene editing to understand which
bacterial genes are essential for symbiosis. By the final week, you’ll design your own
experiment, analyze data, and present discoveries like professional scientists.
What You’ll Learn: This cluster bridges microbiology, genetics, developmental biology,
and evolution. You’ll master laboratory techniques including sterile culturing, PCR,
microscopy (light and electron), and genetic analysis. Beyond technical skills, you’ll
learn to think like a scientist: asking questions, designing experiments, troubleshooting
problems, and communicating findings. You’ll explore symbiosis, host-microbe
interactions, bioluminescence, and evolutionary adaptation.
Why This Matters: Understanding beneficial bacteria is transforming modern medicine
and biotechnology. Your body contains trillions of bacteria influencing digestion,
immunity, and brain function. The microbiome revolution is changing how we develop
probiotics, fight antibiotic resistance, and treat diseases from IBD to depression. The
squid-Vibrio system has led to breakthrough discoveries about animal-bacteria
communication, with applications in biosensors, biofuel production, coral reef protection,
and understanding immune system function. Skills gained here prepare you for careers
in medicine, biotechnology, marine biology, and microbiology.
Course content and structure
This cluster will provide a variety of modules that will cover topics in microbial genetics,
molecular and developmental biology, and experimental evolution. The course will be
divided into 4 week modules during the month long cluster. We plan on using both case
studies and in class activities as well as laboratory sessions for students to gain hands
on experiences in working with both microbes and dumpling squids.
Preliminary schedule
Week 1: Microbiological techniques- We will cover various aspects of microbes and how
they associate with various hosts (both plant and animal).
Sterile technique, plating, streaking, growing cultures
Identification of microbes through PCR
Cloning, sequence analysis
Week 2: Microscopy and Development
Prepping samples for light and SEM
Visualizing changes in morphology
Identifying genes that are involved in morphological changes
Week 3:
Mutational knock outs in V. fischeri
CRISPR cas-9
Triparental mating/conjugation
Infection/colonization experiments
Week 4:
Analysis of animal infection studies
Analysis of single cell libraries
Data annotation and verification of mutants