classroom activities
sporte | November 21, 2008There's no question that the ability to work with information is one that will be required and valued for a long time to come. I think it's imperative for teachers to have students practice this skill whenever an opportunity comes about. The problem for many teachers is finding the time to identify good data sets.
MRSA stands for Methicillin-resistant Staphylococcus aureus (MRSA), a serious problem for hospital patients. Six of out seven people who become infected with MRSA, get it from some kind of health-care facility. In 2007, the CDC issued a report claiming that 18,000 people die every…
sporte | November 15, 2008If you're going to create a new life form (even if it's only digital), Sunday Saturday seems like the best day to give it a try.
Reposted from an earlier year.
Build-A-Virus is a quick, fun, and simple game that was created and put on-line by Bioreliance, now owned by Invitrogen. This game is lots of fun, even when your students are college instructors.
In this activity, you create a new virus by picking different physical characteristics.
The game works like this:
First, you choose whether the virus has an envelope or not.
Next, you choose whether the genome is single or double-…
sporte | November 9, 2008It was a wet and rainy day yesterday, and we have a dissecting microscope, so I decided to see if I could find some tardigrades.
Tardigrade photo by nebarnix
Reposted from Nov. 2006
I went outside and scraped a bit of moss and some lichens off of our deck. Then I put the lichens and moss in a dish. We don't have distilled water in our house, so I added a bit of cool some tap water to the dish. I squeezed the moss and lichens in the water. Then I took a pipette and transferred a bit of the stuff in the water to a plastic petri dish and looked for tardigrades.
Sure enough, I saw one…
sporte | November 4, 2008This quarter, I'm using a wiki with my bioinformatics class and posting sometimes about the things that I learn.
Two things I've been experimenting with are:
Setting up pages for individual students so they can take notes while they're working.
Embedding a Google form into one of my wiki pages for student assessment.
Here's a diagram showing some of the pages in my bioinformatics class wiki site.
Syllabus: I suppose this reflects on my own lack of organization, but I use the syllabus as a dynamic document, making changes and adding information throughout the course. There are links…
sporte | November 3, 2008Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein?
I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of Parkinson's disease and I could sure use beta testers.
If you'd like to do this, I need you to follow the directions below and afterwards, go to a web form and answer a few questions. Don't worry about getting the wrong answers. I won't know who you are, so I won't know if you answered anything wrong.
If you have any concerns…
sporte | October 26, 2008Experimenting with on-line worksheets
I know some people who always teach their classes the same way, semester after semester, year after year.. Not me. I always want to experiment and try new things.
This fall, I'm experimenting with using a wiki in the classroom, in addition to my blog. This wont be my first wiki experience. We've long used wikis where I work, and I've used them to collaborate with people in different locations, but this is the first time that I'll try one in a teaching situation.
The wikis in my past
My earlier experiences with wikis had convinced me that they would…
sporte | October 1, 2008ScienceBlogs and science bloggers, in general, have enthusiastically supported fund-raising efforts by DonorsChoose for the past two years, and we're doing it once again for 2008.
DonorsChoose works like this: teachers write descriptions of what they want and how they'll use it for teaching, and submit their proposals to DonorsChoose. We pick the projects we like and if you like them, too, you can help get these projects funded.Donate to schools! Win a prize!
Last time I did this, we ended up funding three cool projects in biotechnology education. Students in Mrs. G's classroom in South…
sporte | September 30, 2008HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun.
I learned about HealthMap awhile ago from Mike the Mad Biologist, but I didn't get time to play with the site until today.
Here's an example to see how it works.
How do I use HealthMap?
I begin using HealthMap by changing the number of diseases selected to "none."
Then I scrolled through the list until I found something interesting. I chose "Poisoning." The number of…
sporte | September 26, 2008Let's play anomaly!
Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome.
During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things.
You've got a week to give it a try. Let's see what you find! The method is…
sporte | September 25, 2008Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank
This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.
In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III.…
sporte | September 22, 2008Wow! One of my commenters, Ms. Baker, suggested an entirely new way that scientists can help with science education. The only requirement is that a science class have their own blog.
So, if your science class has a blog, let me know, so I can share the URL and maybe recruit some scientists or at least graduate students, to take a look.
I think this idea is so great! It doesn't involve any kind of traveling and many, many different scientists can participate, thus minimizing volunteer burn out. It also gives students a way to practice writing about what they do and interacting with the…
sporte | September 21, 2008Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune…
sporte | August 25, 2008A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood.
One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think DNA sequencing (well, actually the data analysis) is one of the most interesting things that a class can do as part of a research project. These days, getting started with this kind of project, wouldn't be so hard.
Here's are some ways that I would get started:
Find an existing project where my students could collaborate and get…
sporte | August 22, 2008Two teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced.
I like this story. One of my former students did a project like this for the FDA years ago, sampling fish from the Pike Place Market and identifying them with PCR. He was an intern, though. Here we have students identifying sushi on their own!
Quoting the New York Times article:
They found that one-fourth of the fish samples with…
sporte | August 4, 2008What happens when high school students clone and sequence genomic DNA?
Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of…
sporte | June 9, 2008What are you learning in school?
xkcd has the inside track on the really important stuff.
sporte | May 8, 2008Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example.
Plus, since GAPDH is a highly conserved, it's a great model for looking at evolution.
You can get more information and register here.
The cool thing about plants is that there's lots of material to work with.
sporte | April 26, 2008Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein?
If the structures of the mutant and wild type (normal) proteins have been solved, NCBI has a program called VAST that can be used to align those structures. I have an example here where you can see how a single amino acid change makes influenza resistant to Tamiflu®.
This 4 minute movie below shows how we can obtain those aligned structures from VAST and view them with Cn3D.…
sporte | April 17, 2008In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions.
We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes.
Now, in one of our last projects we are determining where…
sporte | March 13, 2008I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers.
Some of the people who participated in the challenge found out that it was harder than they expected.
Lessons learned
Okay, what did we learn?
1. The community is the best thing about Open Source
The Open Office advocates enjoy a challenge and are truly, quite helpful. That was something that adventure…