Tuesday, May 19, 2015

Research on a Budget, Part I

I currently teach at a private institution with a healthy endowment. How can I possibly say that we do research on a budget? 

Even with a wonderful laboratory and science center to house our program, I still run a lab on a very tight annual allowance for expendables. For my scientist friends out there, we have about 20 kids completing yearlong projects for less than most professional labs spend in a day.

TRUE -  we have received some fancy gifts, such as a fluorescent scope and camera, for which we are eternally grateful.

ALSO TRUE! -  we perform cutting-edge, publishable research that does not require specialized equipment or much $$$.  The methods and models I shall describe are supported generously by companies and non-profit consortia committed to seeing young scholars engaged in "hands on" science. Many of these methods are easily scalable for use in core biology classes with students of all levels (stay tuned for Part V!).

Our primary model systems                                                                                                                      
                                                                                                                          C. elegans

Mammalian Cell Culture



For the moment, I will focus on the merits of Caenorhabditis elegans, our charming lab mascot!

Getting Started?  

Introduction to C. elegans research 

All things C. elegans (genome, protocols...) 

RNA Interference experiments with C. elegans

     ·      Transparent invertebrates
     ·      Inexpensive and easy to grow
     ·      Shares 40% homology with human genome
     ·      RNA interference is extremely easy and effective

Few specialized materials required
     ·      Small petri dishes
     ·      Dissecting scope
     ·      Autoclave
     ·      Incubator set to 180C

Your most basic tabletop autoclave will suffice and good deals on refurbished veterinary autoclaves are available online for ~$2000. 

We’ve also found that small wine coolers (under $100) make very suitable worm incubators.

What else do we love about C. elegans? Gosh, how much time do you have?

Experiments are Simple!

    Step 1:  Plate Bacteria

                                     Step 2: Transfer Worms 

Step 3:  Incubate

                                                                                        Step 4:  Observe

Cool Research Topics!
     ·      Axon regeneration
     ·      Stress / insulin pathways
     ·      Pheromone signaling
     ·      Mechanosensation 
     ·      Chemosensation
     ·      Amyloid beta accumulation
     ·      Autophagy 
     ·      Lifespan, fat deposition, learning…..etc!!!

Room for Creativity & Innovation! 
One student, Seyoung Lee, PA '12, developed this novel vermiculture setup using a 24-well plate. She worked out the optimal reagent volumes and working distance for her scope, wrote up her protocol and passed it on to other students. We still use her system in the lab for experiments requiring worm isolation. 
Thanks, Seyoung!


Did I Mention that Reagents are Cheap?!?
Caenorhabditis Genetics Center (U. Minnesota)
$7 mutants

DNA Learning Center (Cold Spring Harbor Labs, NY)
FREE mutants & RNAi feeding strains

RNAi Experiments are Easy!

1 - Bacterial feeding strain is transformed with a plasmid encoding a target sequence
2 - Bacteria are induced to transcribe RNA's
3 - Worms eat the bacteria
4 - dsRNA's diffuse throughout the worm, interfering with translation of your gene of interest

                                                                                                        (adapted from Boutros & Ahringer, 2008)

The net result is that science has effectively become much, much more democratized!!!


Access to these simple tools has enabled students to ask sophisticated questions at a very young age.  

Stay tuned for next week's post..."What can a student researcher accomplish in a year?"


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