What happens when a group of streptococci stick to cells in your throat and start to make toxins? Your body fights back by making clones. i-9752f1fb3fb5563646d156bb91c1b3b7-strep.gifThe animated video, Fighting Infection by Clonal Selection, from Etsuko Uno and Drew Berry is so good that if I didn't know better, I would ... Read more
Okay, watching some of the other movies makes me realize that I've been very negligent in not uploading ours. Without further ado, here it is. Can you guess the age of the person who made the movie? I'll give you a hint. It wasn't me.Read more
David Ng from The World's Fair has made this wonderful video on public speaking. Or shall we say the funnier side of public speaking? I really enjoyed it! ... Read more
The Periodic Table of Videos from the University of Nottingham has 118 short YouTube clips about the elements. Wired Campus recommended the Sodium clip (below). I liked it, too. It's not quite as funny as Mentos in Diet Coke, and but it's still cute and the narrator has a haircut like Gene Wilder in Young Frankenstein. ... Read more
Students, teachers and scientists converge tommorrow morning from all around the Puget Sound region and elsewhere in Washington to share their experiences and talk about science. The students will present posters, science-themed music, art, drama, and many different types of projects that involved first-hand research and investigation. Scientists from the local biotech companies and research institutions talk with the students and judge the projects. The public viewing time is tomorrow, May 28th, between 9 am-12 noon at the Meydenbauer Center. More information can be found ... Read more
Over 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 ... Read more
In 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 ... Read more
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find in the sequences of 16S ribosomal RNA are related antibiotic resistance. This is related to our ... Read more
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
  1. Build a data set
  2. Align the sequences
  3. Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we' ... Read more
Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both Windows and Mac OS X. ... Read more

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