Projects

Winter 2017

Action Spectrum Team

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L-to-R: Waverly Tseng, Thijs Walbeek (Instructor), and Paul Llannura.

The circadian system of mammals has its own light input pathway, starting from specialized photoreceptors in the retina and ending with stimulation of specific cells in the brain. Photoreceptors  of different types exist in the mammalian eye that are biochemically different, and respond to different wavelengths and light intensities. To describe the properties of these photoreceptors, scientists commonly use a graphic called an “action spectrum” that summarizes the results of many experiments. In this video tutorial, we provide viewers who are interested in circadian biology with an overview of how photoreceptors are studied and a step-by-step demonstration of how an action spectrum is generated, using the mammalian pupil constriction response as an assay.

Common Clock Graphics Team

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L-to-R: Chris Tu, Dr. Takako Noguchi (Instructor), and Mike Lim.

Circadian biologists often need to work as graphic designers, drawing "cartoons" to show the cellular and molecular mechanisms that underlie circadian clocks. New graphics are created as science progresses, or depending on the focus of a particular study. As a result, there are a variety of graphics showing clock components in different ways in different organisms, making it difficult for students to grasp common clock mechanisms.  In this project, we created a single uniform set of graphics to improve students' understanding of transcription-translation feedback loops of circadian clocks across organisms and to reduce scientist’s effort to make new graphics. A downloadable PowerPoint file contains the graphics and explanations of basic clock mechanisms for the fly, mammal, and plant clocks. We designed these graphics so that teachers and researchers can freely edit and use in their classroom and presentations.

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The Finished Product

(Download PowerPoint File)

This is a downloadable PowerPoint file containing the graphics and explanations of basic clock mechanisms for the fly, mammal, and plant clocks. Teachers and researchers can freely edit and use these graphics in their classroom and presentations.

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Interviews Team

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L-to-R: Dr. Erica Schoeller (Instructor), Sarah To, and Erin Johnson.

Each year, the Center for Circadian Biology hosts world-renowned researchers as part of the annual "From Cells to Clinic" Symposium. Students in the BioClock Studio take advantage of this unique opportunity to perform professional quality interviews of top chronobiologists, implementing the Studio's mission of public outreach. Students perform extensive research on the invited speakers and choose a subject whose research they would like to highlight. Interviews provide insights into the current state of circadian research, the career paths of our interviewees, and the experiences that led them to work in circadian biology. This year, students also designed visual representations to animate the research explained by the biologists and enhance the accessibility of circadian concepts to a general audience.

Mammalian Team

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L-to-R: Dr. Ben Sheredos (Instructor), Adreanne Rivera, Stephanie Leon, Maria Villalon-Landeros, Rahil Hamza, Kristen Phung, Cheyenne Schloffman, and Dr. Karen Tonsfeldt (Instructor).

The “Mammalian MegaGroup” created three different educational resources to explain the unique properties of mammalian circadian clocks. The first team created a video introducing the cellular and molecular mechanisms of the central pacemaker neurons in the Suprachiasmatic nucleus (SCN). The second team created a video that reviews classic experiments in the history of the circadian biology that revealed the central role of the SCN in mammals. The third team created an interactive online module in which visitors can puzzle through the steps of experiments that allowed us to comprehend the striking differences between mammalian and bird clocks.

Plant Team

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L-to-R: Dr. Katia Bonaldi (Instructor), Clara Oh, and Jay Dandekar.

Plant flowering is not only an elegant natural wonder but is also a complex biological process. The circadian clock plays a crucial and sophisticated role by allowing the plant to trigger flowering in the proper season. (1) Our first tutorial is designed for a broad audience that would like to understand how plants use their ability to precisely measure the length of day and night to decide when it’s time to flower. This phenomenon is called “Photoperiodic Flowering” (2) The second tutorial is designed for students interested in plant chronobiology. It describes the behind-the-scenes molecular mechanisms by which photoperiodic flowering is achieved in the model plant Arabidopsis. Those mechanisms require the coincidence (i.e. happening at the same time) of two types of regulation, one involving daylight, and the other being clock-driven.

"Small" Projects

In addition to the larger team projects, BioClock Studio 2017 undertook a number of additional projects.

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Symposium Planning

A special feature of the BioClock Studio is the opportunity to participate in the annual “From Cells to Clinic” international symposium hosted by CCB. This project developed an orientation tutorial to show students what to expect, how to execute their roles, and how to get the most out of their conference experience.


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Annotated Articles

Studio participants selected a key article in the history of circadian biology and provided annotatations for AAAS's Science in the Classroom project. 


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Chronopedia

Continuing the work of BioClockStudio 2016, participants wrote, edited, and curated entries for the ongoing Chronopedia project.


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Media

Participants took, edited, and curated the photographs you see on this webpage, and on our social media, documenting the work of BioClock Studio 2017, including our participation at the 2017 "From Cells to Clinic" symposium.


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Poster

Participants created a poster detailing the BioClock Studio's activities and presented it at the 2017 CCB Symposium.

Winter 2016

Luciferase Project

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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

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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

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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

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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

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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

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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 visit 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

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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)
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