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The Characterization and Imaging of Single Molecules and Assays
(CHARISMA) IdeaLab is a forum where students discuss multidisciplinary
approaches to the application and elucidation of biological functions. While
participating projects are unique and may not pursue a common deliverable
product, they share a similar set of challenges. Students from different
backgrounds each have strengths that serve a different subset of these challenges.
Consequently, collaboration promotes mutual success in applications as diverse as
single-molecule genotyping, point-of-care disease diagnostic assays, and fundamental
biopolymer dynamics studies.
In the modern research environment, non-biologists such as engineers, physicists, and
chemists are tasked with employing techniques common among biologists. Likewise,
biologists are tasked with employing new probes and platforms developed by their
colleagues in other fields. Together, these scientists can capitalize on their respective
training to aid one another in implementing tools such as biological binding protocols,
microscale devices, quantum dots and fluorescence microscopy.
While the applications served by the CharISMA Idea Lab are broad and span several
research areas and departments, the shared narrow skill set critical to their success
maintains a sharp focus in the lab. This skill set includes:
Employing fluorophores Fluorescence is the signal of choice for single molecule
studies and assays. Various fluorophores are used to stain biological macromolecules or
cells and fluorescent nanoparticles or quantum dots are used as tags for complimentary
components. These may exhibit photobleaching, photocleavage and blinking to varying
degrees.
Employing receptor-ligand pairs These ubiquitous complimentary molecules, such as
streptavidin-biotin or antigen-antibody, act as tether linkages for single molecule work or
recognition elements for assays.
Implementing surface treatments Surfaces contacting samples must be treated to
promote or prevent the adhesion of biological components and fluorophores.
Signal recognition and image analysis The image acquisition rate of
fluorescence intensity must be commensurate with the timescale of observed events and the
images then processes to extract information and compute statistics.
Together, the idea lab members compile, share, and improve upon protocols to
address the above issues and many others for old and new systems in common or novel
environments. These issues are crucial to experimental success and important details are
often not included in published literature. Many students are the first or only members of
their research group facing these challenges. Due to the interdisciplinary nature of this
work, students must look outside their departments for assistance and collaboration. The
idea lab brings together students in need of each other’s help who may not have
otherwise been aware of one another. The knowledge base developed by the idea lab
serves students working on current and future projects in:
Single-molecule detection and manipulation< Direct observation of single
biological macromolecules or cells to answer fundamental biological or biophysical
questions.
Microfluidics for biological applications
- Point-of-care lab-on-a-chip devices for diagnostic assays
- Platforms to incubate, probe, trap, or sort biological system components for
fundamental studies
Fluorescent probe development and improvement
Collaborative ventures forged in the idea lab
The idea lab will meets biweekly to share feature presentations on research progress given
by participating members. This allows for the organic interaction of students excited about
the enormous and burgeoning potential of single-molecule studies and biological assays.
Berkeley has world leaders in these fields making it the ideal place for a formal group
committed to realizing the potential of these important tools. This special assembly of
students are aptly suited to nucleate promising new ideas.
The CharISMA idea lab is a discussion forum of common tools used and problems encountered
in related, yet diverse, applications. The group represents researchers doing this important
work at Berkeley and serves as a go-to resource for incoming interested students.
The CharISMA idea lab aims to build knowledge base to serve future students with details
usually not preserved in a central location or format. It provides a supportive environment
for students working otherwise independently on challenging multidisciplinary problems.
Main Contact: Hagar Zohar
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