SBD Modules

composite image of octopus, axolotls, and stumpy cuttlefish
California Two-spot Octopus (Credit Tom Kleindinst), Axolotls (Credit Dee Sullivan), Stumpy Cuttlefish (Kleindinst)

The SBD semester is organized as a series of 4 three-week modules; students chose a single course in each module.  These courses are inspired by the MBL’s world-renown summer Advanced Research Training Courses and are an intense immersion focusing on experiential learning through laboratory research. 

Module 1: Parasitology or TBD
Module 2: Stem Cells and Regeneration or Optics, Waves and Modern Physics or Fundamentals of Synapses
Module 3: BioDiversity or Imaging for Biological Research
Module 4: Dynamic Camouflage or TBD
Cross module courses: Visual Languages or Classic Experiments in Biology

Module 1

(under development)


Kate Rawlinson

This course introduces the diversity of parasitic Protozoa and Metazoa, and explores the morphology, genomics, developmental life cycle, pathology, immunology, epidemiology, and treatment and control of the major parasite groups. The focus will be on aquatic species, including those that cause pathology in humans and other mammals. The course will involve lectures, fieldwork and lab experiments including designing and carrying out an independent research project. The field portion will involve collecting local aquatic snails and identifying parasites that infect other metazoans at different life stages. Lab experiments will focus on parasitic trematode flatworms, both a local, non-infectious, species as well as the opportunity to work on a human pathogenic species. The lab portion will introduce the molecular techniques, resources and microscopy used in contemporary parasitology to investigate gene expression and protein function in the parasites, as well as in parasite-host interactions. These techniques form part of the toolkit used by parasitologists to understand the basic biology of these organisms, an essential step in the search and development of novel therapeutics.

Module 2 (Choose 1 of 3):

Stem Cells and Regeneration: From Aquatic Research Organisms to Mammals

This course will explore contemporary stem cell biology and regeneration with emphasis on molecular mechanisms and applications, and will cover the history of stem cell discoveries through the latest advances, including genome-wide profiling, and targeted gene editing.  A focus of the course will be around how discoveries in aquatic research organisms have driven the progress in regeneration biology.  The lab portion of the course will introduce and provide hands-on experience on experimental approaches and techniques used in cell biology, development, and regeneration research. There will be a focus on microscopy (brightfield, fluorescence, high-resolution microscopy) and use of open source software to analyze images. There will be an introduction into the use of stains, antibodies, and genetically-encoded fluorescent markers to analyze cellular structures in aquatic organisms that include axolotls, Nematostella, worms, cephalopods and zebrafish. In addition, this course will provide hands-on experience on molecular tools to generate DNA constructs and introduce the use of CRISPR as an important tool to knockdown gene function in genetic and non-genetic experimental systems.

Optics, Waves and Modern Physics at MBL 

Patrick LaRiviere and Rudolf Oldenburg

This course, consisting of lecture and extensive inquiry based lab work exploiting opportunities and resources unique to the MBL, is designed to fulfil intermediate-level requirements in Physics for biology majors and those with a pre-med focus.  The course will focus on the physical principles underlying some of the instruments students will use in other portions of the program, such as fluorescence and polarized-light microscopes used in Biodiversity and Imaging, optical principles involved in camouflage and perception, and the acoustic doppler current profilers and chirp-based SONAR systems used in Biological Oceanography. The course will have a significant research and exploration component.

Fundamentals of Synapses

Jennifer Morgan and Joshua Rosenthal

In this course, students will learn about the fundamentals of synapses, from molecular analysis to structure and function. Marine and aquatic models have historically provided a unique opportunity to investigate synaptic function due to the large size of their neurons, including the synaptic connections. Today, these synapse models are used to study basic principles of neuron-to-neuron communication (synaptic transmission), as well as disease mechanisms. In addition to lectures and discussions of key literature, this course will feature hands-on laboratory-based exercises in molecular genetics, imaging, and physiology of synapses, as well as independent "discovery" projects to explore new topics in synapse biology.

Module 3 (Choose 1 of 2):


Andrew Gillis

This course presents an overview of the diversity of living organisms, including archaea, bacteria, single-celled eukaryotes, fungi, plants, and animals, with an emphasis on their evolutionary histories, relationships, and the biological and evolutionary implications of the characteristic features of each group. We will explore how these different lineages have evolved remarkable solutions to challenges in locomotion, metabolism, and life in extreme environments.  Work in the lab will take advantage of the diversity of organisms that live around, or are maintained at, the Marine Biological Laboratory.

Imaging for Biological Research

Louis Kerr and Carsten Wolff

This course will introduce students to the fundamentals of imaging, quickly advancing to cutting edge advances in the field.  The course will focus on use state-of-the art microscopes, with students designing and executing an original research project including data acquisition and analysis using cutting-edge image analysis software.  Students will begin by building their own simple microscopes, and then learn to use confocal and electron microscopes, as well techniques for fixed and live sample preparation.  Lectures and discussion will introduce each topic and highlight limitations and challenges in the field.

Module 4 (Choose 1 of 2):

(under development)

Dynamic Camouflage: Behavior, Visual Perception and Neural Skin Patterning in Cephalopods

Roger Hanlon      

This course takes an integrative approach to understanding a neurally controlled system of dynamic defense against visual predators. Camouflage is a widespread form of defense throughout the animal kingdom in every known habitat. In the oceans, cephalopods (cuttlefish, octopus, squid) have evolved a sophisticated sensorimotor system called Rapid Adaptive Coloration, which can instantaneously change their total body appearance within a fraction of a second to range from highly camouflaged to startlingly conspicuous for a wide range of behaviors. The forms and functions of this dynamic system will be teased apart integrative fashion in a top-down approach from ecology to organismal biology to organs, tissues and cells. The course touches on neural anatomy, sensation, visual perception and animal behavior.