web resources
sporte | November 7, 2006BioMed Central has gone beyond conventional scientific publishing and started including movie supplements to scientific papers. I saw this one in my e-mail box and couldn't resist.
After all, if you don't have access to a microscope, equipped with a digital video camera, how are you supposed to see these sorts of things?
I took a look at the article from Neural Development, from Zolessi, et. al. comparing the development of retinal ganglion cells in vitro and in vivo. In the movie, linked below, the first cell looks a bit like a child playing "Pin the tail on the Donkey." He/She (the…
sporte | November 4, 2006You've probably heard about enterprising researchers attaching cameras to dolphins, dogs, and other animals, in order to learn how things look from the critter-point of view. Now, some enterprising lab rats have added a new twist to this technique.
It's lab cam!
From Attila Csordas , we have a report about researchers documenting their work through film in an unusual way. They put on a funky-looking hat with a digital camera attached and film their hands doing the experiments. There's even a short movie made by John Cumbers from OpenWetWare, on preparing Drosophila embryo chromatin for…
sporte | October 13, 2006Yikes, I've spilled some DHMO on my hands! What do I do now?
Do you know the truth about DHMO?
Look at this web site and tell me if you still want to go swimming.
sporte | October 13, 2006In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed.
Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step.
Picking your trait. If you're having a hard time thinking of a trait, it might be helpful think about where plants grow, why we grow plants, and why it might be hard or easy for plants to grow.
Some of the environmental factors that affect plant growth are: climate, soil composition, nutrient…
sporte | October 10, 2006Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)?
Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools.
If you already know all about ESTs, you might want to jump ahead and read about the activity. If…
sporte | October 5, 2006Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to be invented. So, when I first started giving workshops for teachers on biotechnology and the world of the web, many were quite surprised to find out about the PubMed database.
Since PubMed is (to me) one of the best resources to ever come along, I think we should explore it a…
sporte | October 4, 2006Awhile back Chemical & Engineering News published a fascinating article called "The Secret Life of Plant Crystals" with some wonderful photos of calcium oxalate crystals. Special cells (called "idioblasts") produce these crystals, with shapes that are unique to each type of plant.
Even though 75% of flowering plants make these crystals, no one knows why they make them and in fact, their functions may be as diverse as their shapes. Some crystals look sharp and dangerous, like thistles or thorns, suggesting that they function to defend a plant from hungry herbivores. Other crystals are…
sporte | September 15, 2006Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure.
First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D.
1K9L
If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions also show how to download and open the structure. It's pretty simple once you've given it a try.
Hide a strand
Next, we're going to hide one of the strands. To do this, look in the menu bar for the Show/Hide menu and open…
sporte | September 11, 2006A long time ago, I saw a Star Trek episode where the crew encountered aliens who lived at a different frequency. I may have this backwards, but I think the aliens moved so quickly that no one knew they were there. And until problems struck, our heroes were happily oblivious to the existence of the others.
The Plants In Motion movies remind me of that episode.
Since plant movement occurs much more slowly than movements we can easily observe, we tend to think that plants don't move. These movies prove that idea wrong. Filmed with time-lapse photography, these short movies show seeds…
sporte | September 9, 2006"And it's a hard, and it's a hard, it's a hard, and it's a hard, And it's a hard rain's a-gonna fall. "
- BoB Dylan
Tired of Simpson reruns and the exploits of Friends?
[From the WSTA]
NOVA is broadcasting an entire series of shows on hurricanes, Katrina, and what the experts predicted would happen should a hurricane ever hit New Orleans. Check out the schedule below.
NOVA Presents "Storm That Drowned a City"
Broadcast: Tuesday, September 12, 2006http://www.pbs.org/nova/orleans/
(NOVA airs on PBS at 8 p.m. ET/PT. Check your local listings as
broadcast dates and times may vary. This…
sporte | September 8, 2006Why do I love Cn3D? Let me count the ways.
What does Cn3D do? (Hint: say "Cn3D" out loud).
Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use.
Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier.
An added benefit is that you don't have to try and find old copies of Netscape or other bits of obsolete software…
sporte | September 7, 2006No biology course is complete these days without learning how to do a BLAST search.
Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key.
Development of the tutorial and the activity were supported by funding from the National Science Foundation.
This is reposted from the the original DigitalBio blog.
This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to incorporate student comments and teacher requests. Originally developed for…
sporte | August 31, 2006Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?
Chemical and Engineering News, published by the American Chemical Society, has a wonderful section that you will certainly appreciate.
"What's that stuff?" is a collection of entertaining stories about the stuff we encounter in everyday life. Each article combines chemistry with history and fun facts in a way that entices the reader to stay awhile and read every one.
Since the stories are written for non-chemists, they make a perfect companion to chemistry courses ranging from…
sporte | August 29, 2006The fall soccer season is well underway and the Hummingbirds soccer team is kicking everything in sight. The hummingbirds in these two series of photos are much quicker, considerably smaller and certainly cute.
A friend sent me this link since I manage the Hummingbirds soccer team. Hopefully, the person who posted these shots of baby hummingbirds will leave them up for awhile.
My husband told me about this page at Nature Photography with other truly incredible hummingbird photos. There are some great photos of hummingbirds in mid flight plus some pics of hummingbirds sitting quietly at bird…
sporte | August 28, 2006One of most wonderful things about the Internet has been the emergence of research projects that involve the general public. Universities like Cornell, Kansas University, and the University of Minnesota, to name a few, have established web sites and on-line databases that encourage both students and amateur biologists to participate in biological field studies. Not only do these projects extend the potential for good science by collecting more data, they give visibility to the research process and allow the public to take ownership and contribute to the store of scientific knowledge.
Monarch…
sporte | August 23, 2006We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because (quoting Jerry Garcia):
Power is a scary thing. When you feel that you are close to it, you want to
make sure that it isn't used for misleading. So all this time we've avoided
making any statements about politics, about alignments of any sort.
But the Dead decided deforestation was too big of an issue to ignore and held a press conference at the…
sporte | August 22, 2006Have you ever wondered how people actually go about sequencing a genome?
If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?
Wonder no more!
You too, can take a virtual tour of the Washington University Genome Center.
I found this really excellent series of short videos that follows two genetics students, Libby and Bryce, as they meet on the bus to the Genome Center and learn about all the steps…
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
sporte | July 14, 2006Last week, we embarked on an adventure with BLAST.
BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence, any sequence, from a set of 16 unknown sequences and use BLAST to identify that sequence.
This week, we'll examine the results.
I did the experiment, too, with a completely different unknown sequence that's pasted below. This sequence is not part of the data…