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Have you ever wondered how to find things in the NCBI databases? Maybe you tried to find something but didn’t know how it was spelled. Or maybe you tried to use a common name like “pig” or “deer” to find information in a database, not knowing that all the organism names are in Latin. Or…

Wow! 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…

Meet the ribosomes

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…

How to use Cn3D

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.…

Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we’ll answer in this last video. We’re going to use pivot tables and count all the genera that live in each biome. Then, we’ll…

This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus.

What do you do after you’ve used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What’s the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data…

For the past few years, I’ve been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to…