Projects

Winter 2016

Luciferase Project

project

The luciferase project team is producing a set of videos to help students understand the overall use of reporters as tools in circadian biology, as well as their specific application in cyanobacteria and mammals.  We hope to complete an animated tutorial covering the basics of reporters, as well as a set of in lab videos that detail the use of luciferase and how data is generated from these techniques.

The Finished Products

This video was made for use in an upper division undergraduate class on circadian rhythms and biological clocks at UC San Diego. It explains the molecular mechanisms of the luciferase reporter, and the key differences between the usage of luciferase and green fluorescent protein.

This video shows the in-lab use of luciferase reporters in mice for circadian rhythms research.

This video shows the in-lab use of luciferase reporters in cyanobacteria for circadian rhythms research.

Chronopedia

project

Everything a BIMM116/PSYC133 student will need to feel confident in the “Circadian Rhythms- Biological Clocks” course will be here!  We hope to not only provide explanations of appropriate depth that are study-friendly for all the big topics in circadian biology, but to have plenty of additional resources and content for more casual learners as well.  We're also pursuing an easily moldable index of terms so our website can grow alongside the cutting-edge accomplishments and discoveries of the field itself.

2-Process Sleep

project

The 2-process sleep project team aims to create a short video that portrays the 2-process model of sleep regulation. This video will cover the circadian alerting signal, controlled primarily by the internal circadian clock, as well as the process of sleep homeostasis. Because the 2-process model of sleep regulation is fundamentally applicable to daily lives, this video tutorial targets the general public in addition to the BIMM116/PSYC133 students.

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The Finished Product

This tutorial was produced by members of the BioClock Studio Winter 2016 at UC San Diego, and clarifies how sleep homeostasis and the circadian clock are hypothesized to interact to determine the sleep-wake cycle.

Mammalian Retina and Photoreceptors

project

From basic anatomy of the mammalian retina, to the specific photoreceptors that are responsible for receiving light and relaying such an information to the brain for further interpretation, our project introduces how light can be utilized to produce graphic representation of the environment, as well as to act as a time cue of the circadian rhythm for mammals.

The Finished Product

This tutorial video was produced by members of the BioClock Studio Winter 2016 at UC San Diego and clarifies the anatomy and function of neural circuits for image-forming and non-image-forming vision.

Cyanobacterial Clock Animations

project

The goal of the cyanobacteria clock animation project is to enhance scientific understanding and accessibility of the circadian biology curriculum. Our approach for that goal is through the production of visual materials and resources in description of the oscillator process and output of the cyanobacteria circadian clock.

The Finished Products

This animation demonstrates the circadian oscillator mechanism in the cyanobacterium Synechococcus elongatus.

This animation shows how the core circadian oscillator in the cyanobacterium Synechococcus elongatus sends output to regulate the timing of other intracellular processes.

Website Team

project

The focus of our team is to build and organize this web page in such a way that allows for simple and intuitive navigation. This web page was created to store and archive all of the work that has been done in the Bioclocks Studio and present them to the public to promote the circadian biology.

Winter 2015

Tutorials on Basic Concepts

In the inaugural Winter 2015 BioClock Studio, we asked four participants (Mary Ilyaich, Jenny Lee, Jonathan Loi and Michael Maya-Pienl) to help us identify some central concepts in circadian biology that can be difficult for novices to master. As a group, we spent hours discussing how best to explain these concepts, with students telling us what worked and what didn't. With these student-centered recommendations in hand, Drs. Liz Harrison and Ben Sheredos (trainees in the Center for Circadian Biology at the time) set out to create new educational materials. The resulting videos, shown below, have proven to be very useful for those seeking an overview of some of circadian biology's most basic concepts.

The Finished Products

An Introduction to Free-Running Periods.

An Introduction to Naming Conventions.

An Introduction to Phase Response Curves.

Interviews at the CCB Symposium

Public outreach is a central aim of the BioClock Studio, and UC San Diego provides unique opportunities to accomplish this aim. Every year, the Center for Circadian Biology hosts researchers from around the world as part of the annual "From Cells to Clinic" Symposium. In the Winter 2015 BioClock Studio, students set the ambitious goal of interviewing three world-class researchers during their visist to the symposium. The Interviews provide insight into the current state of circadian research, the career paths of our interviewees, and the experiences that led them to work in circadian biology.

  • Team Leader: Dr. Pagkapol Yhew Pongsawakul
  • Students who planned and conducted the interviews:
    • Raveena Bakhru
    • Jacqueline Chan
    • Lucy Wu
  • Support: 
    • Dr. Madeleine Picciotto (training in professional interviewing skills)
    • Craig Bentley & Educational Technology Services (filming and production)

The Finished Products

An Interview with Dr. Katema Paul

(Morehouse School of Medicine).

An Interview with Dr. Phyllis Zee

(Northwestern University Institute for Neuroscience).

An Interview with Dr. Carrie Partch

(UC Santa Cruz Chemistry Department).

In-Lab Videos of Circadian Research Techniques

The In-Lab Video team created a set of videos for the purpose of demystifying the techniques that are used in circadian research on rodents. These videos give students a look at the hands-on practices of working scientists, providing a grounded understanding of the "Actogram" as a popular method of representing data in circadian biology.

  • Team Leader: Dr. Susan Cohen
  • Students who planned and produced the videos:
    • Tiana Diaz
    • Mary Ilyaich
    • Jenny Lee
  • Support: 
    • The Gorman Lab (demonstrating lab techniques)
      • Deborah May
      • Dr. Liz Harrison
      • Dr. Takako Noguchi
      • Dr. Michael Gorman
    • Craig Bentley & Educational Technology Services (filming and production)

The Finished Products

Setting up a Wheel-Running Experiment

Performing a Wheel-Running Experiment

Analyzing Wheel-Running Data

Understanding the Actogram

Interviews with Circadian Researchers

Public Outreach

Outreach2015

The BioClock Studio needed to establish its public face, and especially its presence on social media. The Public Outreach Team not only laid the groundwork for the website you are viewing now, but also established and managed our YouTube channel, Twitter handle, and Facebook page. Further, they created and presented a Poster at the Center for Circadian Biology's "From Cells to Clinic" Symposium, introducing the BioClock Studio to the global community of researchers in circadian biology.

  • Team Leader: Dr. Susan Golden
  • Students:
    • Jafar Essayli
    • Curie Kim
    • Micael Maya-Pienl
    • Yi-Jung (Emily) Zhang

An Introduction to Circadian Biology

The "Review Team" set the ambitious goal of writing a basic introduction to circadian biology, from scratch. This involved reading a number of pre-existing introductory texts and evaluating what worked and what didn't, from a student's perspective. These student-centered evaluations led to a detailed outline of what an ideal introductory text would look like. Students then spent weeks drafting and revising their own text. The finished product is now live, here on the BioClock Studio website, where anyone can access it to receive an Introduction to Chronobiology.

  • Team Leader: Dr. Ben Sheredos
  • Students:
    • Kathleen Kao
    • Jonathan Loi
    • Hailey Sanden
  • Suppport: Dr. Madeline Picciotto (training in different genres of scientific writing)