This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.) Did they clone or not clone? That is the question. ... Read more
Yesterday morning I was sitting at conference table, downing coffee to keep my eyes open, when I heard someone say that it's springtime now and the snakes are waking up. Well, those kinds of statements at the breakfast table do have a way of getting my attention.
I turned sideways and realized the words were coming from a high school science teacher, that I know, from Arizona.
"Sure," she said, "and people who move here in the winter time are pretty surprised when a snake wakes up and crawls out from under their porch."
A few ... 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
Conflicts between predators like cougars and coyotes and human companions like pets and small children are becoming more common as people move into areas that used to be wildlife habitat.
The Seattle Times has a great story this morning about biologists in Washington who are studying cougars to learn if cougars and people can coexist. The biologists think most of the trouble might be caused by teenage male cougars who move in to the territory when the older, smarter males get killed.
There's also a ... Read more
I 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.
Okay, what did we learn?
1. The community is the ... Read more
Your canopy is disappearing, you're likely to freeze.
NASA's Earth Observatory reports that over 1,110 acres of forest were illegally logged, during the past four years, in the Monarch Butterfly Biosphere Reserve in central Mexico.
Monarch butterflies travel here from all over the United States and Canada. Images from the Ikonos satellite tell us though, that future migrating butterflies are likely have problems in this reserve. The top image is from 2004, the bottom image shows what things are ... Read more
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend.
How do they do it?
Each of the EOS satellites delivers a terabyte or more of data per day from many different instruments.
How do they take satellite imagery, rainfall statistics, temperature information, and other kinds of data and assemble these data into meaningful pictures ... Read more
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.
The parts of this series are:
I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three).
II. ... Read more
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 entry errors and spelling mistakes.
The parts of this series are:
I. Downloading the data from iFinch and preparing it for analysis. (this is the ... Read more